Job ID = 1292889 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T11:55:23 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T11:55:23 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR8176704/SRR8176704.1' 2019-06-02T11:55:23 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_db_type().VDBManagerOpenDBRead( 'SRR8176704' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T11:55:23 fasterq-dump.2.9.6 err: invalid accession 'SRR8176704' 2019-06-02T12:05:52 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T12:05:53 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 34,633,057 reads read : 69,266,114 reads written : 69,266,114 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:37:12 34633057 reads; of these: 34633057 (100.00%) were paired; of these: 1537762 (4.44%) aligned concordantly 0 times 28364913 (81.90%) aligned concordantly exactly 1 time 4730382 (13.66%) aligned concordantly >1 times ---- 1537762 pairs aligned concordantly 0 times; of these: 789855 (51.36%) aligned discordantly 1 time ---- 747907 pairs aligned 0 times concordantly or discordantly; of these: 1495814 mates make up the pairs; of these: 878201 (58.71%) aligned 0 times 380636 (25.45%) aligned exactly 1 time 236977 (15.84%) aligned >1 times 98.73% overall alignment rate Time searching: 00:37:12 Overall time: 00:37:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 28 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 513693 / 33863681 = 0.0152 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 02 Jun 2019 22:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 22:17:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:17:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 22:17:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:17:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 22:17:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:17:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:17:19: 1000000 INFO @ Sun, 02 Jun 2019 22:17:22: 1000000 INFO @ Sun, 02 Jun 2019 22:17:22: 1000000 INFO @ Sun, 02 Jun 2019 22:17:26: 2000000 INFO @ Sun, 02 Jun 2019 22:17:32: 2000000 INFO @ Sun, 02 Jun 2019 22:17:32: 2000000 INFO @ Sun, 02 Jun 2019 22:17:33: 3000000 INFO @ Sun, 02 Jun 2019 22:17:40: 4000000 INFO @ Sun, 02 Jun 2019 22:17:42: 3000000 INFO @ Sun, 02 Jun 2019 22:17:42: 3000000 INFO @ Sun, 02 Jun 2019 22:17:46: 5000000 INFO @ Sun, 02 Jun 2019 22:17:51: 4000000 INFO @ Sun, 02 Jun 2019 22:17:51: 4000000 INFO @ Sun, 02 Jun 2019 22:17:53: 6000000 INFO @ Sun, 02 Jun 2019 22:18:00: 7000000 INFO @ Sun, 02 Jun 2019 22:18:01: 5000000 INFO @ Sun, 02 Jun 2019 22:18:01: 5000000 INFO @ Sun, 02 Jun 2019 22:18:06: 8000000 INFO @ Sun, 02 Jun 2019 22:18:11: 6000000 INFO @ Sun, 02 Jun 2019 22:18:11: 6000000 INFO @ Sun, 02 Jun 2019 22:18:13: 9000000 INFO @ Sun, 02 Jun 2019 22:18:20: 10000000 INFO @ Sun, 02 Jun 2019 22:18:20: 7000000 INFO @ Sun, 02 Jun 2019 22:18:21: 7000000 INFO @ Sun, 02 Jun 2019 22:18:27: 11000000 INFO @ Sun, 02 Jun 2019 22:18:30: 8000000 INFO @ Sun, 02 Jun 2019 22:18:30: 8000000 INFO @ Sun, 02 Jun 2019 22:18:33: 12000000 INFO @ Sun, 02 Jun 2019 22:18:40: 9000000 INFO @ Sun, 02 Jun 2019 22:18:40: 9000000 INFO @ Sun, 02 Jun 2019 22:18:40: 13000000 INFO @ Sun, 02 Jun 2019 22:18:47: 14000000 INFO @ Sun, 02 Jun 2019 22:18:49: 10000000 INFO @ Sun, 02 Jun 2019 22:18:50: 10000000 INFO @ Sun, 02 Jun 2019 22:18:53: 15000000 INFO @ Sun, 02 Jun 2019 22:18:58: 11000000 INFO @ Sun, 02 Jun 2019 22:18:59: 11000000 INFO @ Sun, 02 Jun 2019 22:19:00: 16000000 INFO @ Sun, 02 Jun 2019 22:19:07: 17000000 INFO @ Sun, 02 Jun 2019 22:19:08: 12000000 INFO @ Sun, 02 Jun 2019 22:19:09: 12000000 INFO @ Sun, 02 Jun 2019 22:19:14: 18000000 INFO @ Sun, 02 Jun 2019 22:19:17: 13000000 INFO @ Sun, 02 Jun 2019 22:19:18: 13000000 INFO @ Sun, 02 Jun 2019 22:19:21: 19000000 INFO @ Sun, 02 Jun 2019 22:19:26: 14000000 INFO @ Sun, 02 Jun 2019 22:19:27: 14000000 INFO @ Sun, 02 Jun 2019 22:19:28: 20000000 INFO @ Sun, 02 Jun 2019 22:19:35: 21000000 INFO @ Sun, 02 Jun 2019 22:19:35: 15000000 INFO @ Sun, 02 Jun 2019 22:19:36: 15000000 INFO @ Sun, 02 Jun 2019 22:19:42: 22000000 INFO @ Sun, 02 Jun 2019 22:19:44: 16000000 INFO @ Sun, 02 Jun 2019 22:19:45: 16000000 INFO @ Sun, 02 Jun 2019 22:19:48: 23000000 INFO @ Sun, 02 Jun 2019 22:19:53: 17000000 INFO @ Sun, 02 Jun 2019 22:19:54: 17000000 INFO @ Sun, 02 Jun 2019 22:19:55: 24000000 INFO @ Sun, 02 Jun 2019 22:20:02: 25000000 INFO @ Sun, 02 Jun 2019 22:20:02: 18000000 INFO @ Sun, 02 Jun 2019 22:20:03: 18000000 INFO @ Sun, 02 Jun 2019 22:20:08: 26000000 INFO @ Sun, 02 Jun 2019 22:20:11: 19000000 INFO @ Sun, 02 Jun 2019 22:20:12: 19000000 INFO @ Sun, 02 Jun 2019 22:20:15: 27000000 INFO @ Sun, 02 Jun 2019 22:20:20: 20000000 INFO @ Sun, 02 Jun 2019 22:20:22: 28000000 INFO @ Sun, 02 Jun 2019 22:20:22: 20000000 INFO @ Sun, 02 Jun 2019 22:20:28: 29000000 INFO @ Sun, 02 Jun 2019 22:20:29: 21000000 INFO @ Sun, 02 Jun 2019 22:20:31: 21000000 INFO @ Sun, 02 Jun 2019 22:20:35: 30000000 INFO @ Sun, 02 Jun 2019 22:20:38: 22000000 INFO @ Sun, 02 Jun 2019 22:20:39: 22000000 INFO @ Sun, 02 Jun 2019 22:20:42: 31000000 INFO @ Sun, 02 Jun 2019 22:20:47: 23000000 INFO @ Sun, 02 Jun 2019 22:20:48: 23000000 INFO @ Sun, 02 Jun 2019 22:20:48: 32000000 INFO @ Sun, 02 Jun 2019 22:20:55: 33000000 INFO @ Sun, 02 Jun 2019 22:20:56: 24000000 INFO @ Sun, 02 Jun 2019 22:20:57: 24000000 INFO @ Sun, 02 Jun 2019 22:21:01: 34000000 INFO @ Sun, 02 Jun 2019 22:21:06: 25000000 INFO @ Sun, 02 Jun 2019 22:21:06: 25000000 INFO @ Sun, 02 Jun 2019 22:21:08: 35000000 INFO @ Sun, 02 Jun 2019 22:21:14: 36000000 INFO @ Sun, 02 Jun 2019 22:21:15: 26000000 INFO @ Sun, 02 Jun 2019 22:21:16: 26000000 INFO @ Sun, 02 Jun 2019 22:21:21: 37000000 INFO @ Sun, 02 Jun 2019 22:21:24: 27000000 INFO @ Sun, 02 Jun 2019 22:21:25: 27000000 INFO @ Sun, 02 Jun 2019 22:21:28: 38000000 INFO @ Sun, 02 Jun 2019 22:21:34: 28000000 INFO @ Sun, 02 Jun 2019 22:21:35: 39000000 INFO @ Sun, 02 Jun 2019 22:21:35: 28000000 INFO @ Sun, 02 Jun 2019 22:21:41: 40000000 INFO @ Sun, 02 Jun 2019 22:21:43: 29000000 INFO @ Sun, 02 Jun 2019 22:21:44: 29000000 INFO @ Sun, 02 Jun 2019 22:21:48: 41000000 INFO @ Sun, 02 Jun 2019 22:21:52: 30000000 INFO @ Sun, 02 Jun 2019 22:21:53: 30000000 INFO @ Sun, 02 Jun 2019 22:21:54: 42000000 INFO @ Sun, 02 Jun 2019 22:22:01: 31000000 INFO @ Sun, 02 Jun 2019 22:22:01: 43000000 INFO @ Sun, 02 Jun 2019 22:22:02: 31000000 INFO @ Sun, 02 Jun 2019 22:22:08: 44000000 INFO @ Sun, 02 Jun 2019 22:22:10: 32000000 INFO @ Sun, 02 Jun 2019 22:22:12: 32000000 INFO @ Sun, 02 Jun 2019 22:22:14: 45000000 INFO @ Sun, 02 Jun 2019 22:22:19: 33000000 INFO @ Sun, 02 Jun 2019 22:22:21: 46000000 INFO @ Sun, 02 Jun 2019 22:22:21: 33000000 INFO @ Sun, 02 Jun 2019 22:22:27: 47000000 INFO @ Sun, 02 Jun 2019 22:22:27: 34000000 INFO @ Sun, 02 Jun 2019 22:22:30: 34000000 INFO @ Sun, 02 Jun 2019 22:22:34: 48000000 INFO @ Sun, 02 Jun 2019 22:22:36: 35000000 INFO @ Sun, 02 Jun 2019 22:22:39: 35000000 INFO @ Sun, 02 Jun 2019 22:22:40: 49000000 INFO @ Sun, 02 Jun 2019 22:22:45: 36000000 INFO @ Sun, 02 Jun 2019 22:22:46: 50000000 INFO @ Sun, 02 Jun 2019 22:22:48: 36000000 INFO @ Sun, 02 Jun 2019 22:22:53: 51000000 INFO @ Sun, 02 Jun 2019 22:22:54: 37000000 INFO @ Sun, 02 Jun 2019 22:22:57: 37000000 INFO @ Sun, 02 Jun 2019 22:22:59: 52000000 INFO @ Sun, 02 Jun 2019 22:23:03: 38000000 INFO @ Sun, 02 Jun 2019 22:23:06: 53000000 INFO @ Sun, 02 Jun 2019 22:23:06: 38000000 INFO @ Sun, 02 Jun 2019 22:23:12: 39000000 INFO @ Sun, 02 Jun 2019 22:23:12: 54000000 INFO @ Sun, 02 Jun 2019 22:23:15: 39000000 INFO @ Sun, 02 Jun 2019 22:23:19: 55000000 INFO @ Sun, 02 Jun 2019 22:23:21: 40000000 INFO @ Sun, 02 Jun 2019 22:23:24: 40000000 INFO @ Sun, 02 Jun 2019 22:23:26: 56000000 INFO @ Sun, 02 Jun 2019 22:23:30: 41000000 INFO @ Sun, 02 Jun 2019 22:23:32: 57000000 INFO @ Sun, 02 Jun 2019 22:23:34: 41000000 INFO @ Sun, 02 Jun 2019 22:23:39: 42000000 INFO @ Sun, 02 Jun 2019 22:23:39: 58000000 INFO @ Sun, 02 Jun 2019 22:23:43: 42000000 INFO @ Sun, 02 Jun 2019 22:23:45: 59000000 INFO @ Sun, 02 Jun 2019 22:23:48: 43000000 INFO @ Sun, 02 Jun 2019 22:23:52: 43000000 INFO @ Sun, 02 Jun 2019 22:23:52: 60000000 INFO @ Sun, 02 Jun 2019 22:23:56: 44000000 INFO @ Sun, 02 Jun 2019 22:23:59: 61000000 INFO @ Sun, 02 Jun 2019 22:24:01: 44000000 INFO @ Sun, 02 Jun 2019 22:24:05: 45000000 INFO @ Sun, 02 Jun 2019 22:24:05: 62000000 INFO @ Sun, 02 Jun 2019 22:24:10: 45000000 INFO @ Sun, 02 Jun 2019 22:24:12: 63000000 INFO @ Sun, 02 Jun 2019 22:24:14: 46000000 INFO @ Sun, 02 Jun 2019 22:24:18: 64000000 INFO @ Sun, 02 Jun 2019 22:24:19: 46000000 INFO @ Sun, 02 Jun 2019 22:24:23: 47000000 INFO @ Sun, 02 Jun 2019 22:24:25: 65000000 INFO @ Sun, 02 Jun 2019 22:24:28: 47000000 INFO @ Sun, 02 Jun 2019 22:24:31: 48000000 INFO @ Sun, 02 Jun 2019 22:24:31: 66000000 INFO @ Sun, 02 Jun 2019 22:24:36: 48000000 INFO @ Sun, 02 Jun 2019 22:24:38: 67000000 INFO @ Sun, 02 Jun 2019 22:24:40: 49000000 INFO @ Sun, 02 Jun 2019 22:24:40: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:24:40: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:24:40: #1 total tags in treatment: 32585734 INFO @ Sun, 02 Jun 2019 22:24:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:24:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:24:41: #1 tags after filtering in treatment: 28288878 INFO @ Sun, 02 Jun 2019 22:24:41: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 02 Jun 2019 22:24:41: #1 finished! INFO @ Sun, 02 Jun 2019 22:24:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:24:43: #2 number of paired peaks: 123 WARNING @ Sun, 02 Jun 2019 22:24:43: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sun, 02 Jun 2019 22:24:43: start model_add_line... INFO @ Sun, 02 Jun 2019 22:24:44: start X-correlation... INFO @ Sun, 02 Jun 2019 22:24:44: end of X-cor INFO @ Sun, 02 Jun 2019 22:24:44: #2 finished! INFO @ Sun, 02 Jun 2019 22:24:44: #2 predicted fragment length is 55 bps INFO @ Sun, 02 Jun 2019 22:24:44: #2 alternative fragment length(s) may be 2,55,124,133,136,147 bps INFO @ Sun, 02 Jun 2019 22:24:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.05_model.r WARNING @ Sun, 02 Jun 2019 22:24:44: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:24:44: #2 You may need to consider one of the other alternative d(s): 2,55,124,133,136,147 WARNING @ Sun, 02 Jun 2019 22:24:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:24:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:24:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:24:45: 49000000 INFO @ Sun, 02 Jun 2019 22:24:49: 50000000 INFO @ Sun, 02 Jun 2019 22:24:54: 50000000 INFO @ Sun, 02 Jun 2019 22:24:57: 51000000 INFO @ Sun, 02 Jun 2019 22:25:03: 51000000 INFO @ Sun, 02 Jun 2019 22:25:06: 52000000 INFO @ Sun, 02 Jun 2019 22:25:12: 52000000 INFO @ Sun, 02 Jun 2019 22:25:15: 53000000 INFO @ Sun, 02 Jun 2019 22:25:21: 53000000 INFO @ Sun, 02 Jun 2019 22:25:23: 54000000 INFO @ Sun, 02 Jun 2019 22:25:30: 54000000 INFO @ Sun, 02 Jun 2019 22:25:32: 55000000 INFO @ Sun, 02 Jun 2019 22:25:39: 55000000 INFO @ Sun, 02 Jun 2019 22:25:41: 56000000 INFO @ Sun, 02 Jun 2019 22:25:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:25:48: 56000000 INFO @ Sun, 02 Jun 2019 22:25:50: 57000000 INFO @ Sun, 02 Jun 2019 22:25:57: 57000000 INFO @ Sun, 02 Jun 2019 22:25:59: 58000000 INFO @ Sun, 02 Jun 2019 22:26:07: 58000000 INFO @ Sun, 02 Jun 2019 22:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.05_summits.bed INFO @ Sun, 02 Jun 2019 22:26:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (655 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:26:08: 59000000 INFO @ Sun, 02 Jun 2019 22:26:16: 59000000 INFO @ Sun, 02 Jun 2019 22:26:17: 60000000 INFO @ Sun, 02 Jun 2019 22:26:25: 60000000 INFO @ Sun, 02 Jun 2019 22:26:25: 61000000 INFO @ Sun, 02 Jun 2019 22:26:33: 61000000 INFO @ Sun, 02 Jun 2019 22:26:34: 62000000 INFO @ Sun, 02 Jun 2019 22:26:42: 62000000 INFO @ Sun, 02 Jun 2019 22:26:43: 63000000 INFO @ Sun, 02 Jun 2019 22:26:51: 63000000 INFO @ Sun, 02 Jun 2019 22:26:52: 64000000 INFO @ Sun, 02 Jun 2019 22:27:00: 64000000 INFO @ Sun, 02 Jun 2019 22:27:02: 65000000 INFO @ Sun, 02 Jun 2019 22:27:08: 65000000 INFO @ Sun, 02 Jun 2019 22:27:11: 66000000 INFO @ Sun, 02 Jun 2019 22:27:17: 66000000 INFO @ Sun, 02 Jun 2019 22:27:20: 67000000 INFO @ Sun, 02 Jun 2019 22:27:24: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:27:24: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:27:24: #1 total tags in treatment: 32585734 INFO @ Sun, 02 Jun 2019 22:27:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:27:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:27:24: #1 tags after filtering in treatment: 28288878 INFO @ Sun, 02 Jun 2019 22:27:24: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 02 Jun 2019 22:27:24: #1 finished! INFO @ Sun, 02 Jun 2019 22:27:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:27:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:27:26: 67000000 INFO @ Sun, 02 Jun 2019 22:27:27: #2 number of paired peaks: 123 WARNING @ Sun, 02 Jun 2019 22:27:27: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sun, 02 Jun 2019 22:27:27: start model_add_line... INFO @ Sun, 02 Jun 2019 22:27:27: start X-correlation... INFO @ Sun, 02 Jun 2019 22:27:27: end of X-cor INFO @ Sun, 02 Jun 2019 22:27:27: #2 finished! INFO @ Sun, 02 Jun 2019 22:27:27: #2 predicted fragment length is 55 bps INFO @ Sun, 02 Jun 2019 22:27:27: #2 alternative fragment length(s) may be 2,55,124,133,136,147 bps INFO @ Sun, 02 Jun 2019 22:27:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.20_model.r WARNING @ Sun, 02 Jun 2019 22:27:27: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:27:27: #2 You may need to consider one of the other alternative d(s): 2,55,124,133,136,147 WARNING @ Sun, 02 Jun 2019 22:27:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:27:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:27:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:27:29: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:27:29: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:27:29: #1 total tags in treatment: 32585734 INFO @ Sun, 02 Jun 2019 22:27:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:27:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:27:30: #1 tags after filtering in treatment: 28288878 INFO @ Sun, 02 Jun 2019 22:27:30: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 02 Jun 2019 22:27:30: #1 finished! INFO @ Sun, 02 Jun 2019 22:27:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:27:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:27:32: #2 number of paired peaks: 123 WARNING @ Sun, 02 Jun 2019 22:27:32: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sun, 02 Jun 2019 22:27:32: start model_add_line... INFO @ Sun, 02 Jun 2019 22:27:32: start X-correlation... INFO @ Sun, 02 Jun 2019 22:27:32: end of X-cor INFO @ Sun, 02 Jun 2019 22:27:32: #2 finished! INFO @ Sun, 02 Jun 2019 22:27:32: #2 predicted fragment length is 55 bps INFO @ Sun, 02 Jun 2019 22:27:32: #2 alternative fragment length(s) may be 2,55,124,133,136,147 bps INFO @ Sun, 02 Jun 2019 22:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.10_model.r WARNING @ Sun, 02 Jun 2019 22:27:32: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:27:32: #2 You may need to consider one of the other alternative d(s): 2,55,124,133,136,147 WARNING @ Sun, 02 Jun 2019 22:27:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:27:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:28:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:28:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:28:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:28:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:28:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.20_summits.bed INFO @ Sun, 02 Jun 2019 22:28:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (156 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:28:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:28:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:28:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996819/SRX4996819.10_summits.bed INFO @ Sun, 02 Jun 2019 22:28:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (400 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。