Job ID = 1299951 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:35:45 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' 2019-06-03T09:35:45 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/traces/sra36/SRR/001146/SRR1174468' 2019-06-03T09:35:45 fasterq-dump.2.9.6 err: invalid accession 'SRR1174468' 2019-06-03T09:37:54 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 ) 2019-06-03T09:37:54 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 ) 2019-06-03T09:39:19 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 ) 2019-06-03T09:48:54 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 : 33,101,581 reads read : 66,203,162 reads written : 66,203,162 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: 01:31:38 33101581 reads; of these: 33101581 (100.00%) were paired; of these: 2604539 (7.87%) aligned concordantly 0 times 21146494 (63.88%) aligned concordantly exactly 1 time 9350548 (28.25%) aligned concordantly >1 times ---- 2604539 pairs aligned concordantly 0 times; of these: 421991 (16.20%) aligned discordantly 1 time ---- 2182548 pairs aligned 0 times concordantly or discordantly; of these: 4365096 mates make up the pairs; of these: 3182459 (72.91%) aligned 0 times 704501 (16.14%) aligned exactly 1 time 478136 (10.95%) aligned >1 times 95.19% overall alignment rate Time searching: 01:31:38 Overall time: 01:31:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 28 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2579397 / 30866913 = 0.0836 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 @ Mon, 03 Jun 2019 21:05:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 21:05:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:05:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:05:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 21:05:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:05:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:05:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 21:05:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:05:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:06:05: 1000000 INFO @ Mon, 03 Jun 2019 21:06:05: 1000000 INFO @ Mon, 03 Jun 2019 21:06:06: 1000000 INFO @ Mon, 03 Jun 2019 21:06:14: 2000000 INFO @ Mon, 03 Jun 2019 21:06:14: 2000000 INFO @ Mon, 03 Jun 2019 21:06:15: 2000000 INFO @ Mon, 03 Jun 2019 21:06:23: 3000000 INFO @ Mon, 03 Jun 2019 21:06:23: 3000000 INFO @ Mon, 03 Jun 2019 21:06:24: 3000000 INFO @ Mon, 03 Jun 2019 21:06:31: 4000000 INFO @ Mon, 03 Jun 2019 21:06:31: 4000000 INFO @ Mon, 03 Jun 2019 21:06:33: 4000000 INFO @ Mon, 03 Jun 2019 21:06:40: 5000000 INFO @ Mon, 03 Jun 2019 21:06:40: 5000000 INFO @ Mon, 03 Jun 2019 21:06:42: 5000000 INFO @ Mon, 03 Jun 2019 21:06:49: 6000000 INFO @ Mon, 03 Jun 2019 21:06:50: 6000000 INFO @ Mon, 03 Jun 2019 21:06:50: 6000000 INFO @ Mon, 03 Jun 2019 21:06:58: 7000000 INFO @ Mon, 03 Jun 2019 21:06:59: 7000000 INFO @ Mon, 03 Jun 2019 21:06:59: 7000000 INFO @ Mon, 03 Jun 2019 21:07:07: 8000000 INFO @ Mon, 03 Jun 2019 21:07:07: 8000000 INFO @ Mon, 03 Jun 2019 21:07:08: 8000000 INFO @ Mon, 03 Jun 2019 21:07:16: 9000000 INFO @ Mon, 03 Jun 2019 21:07:16: 9000000 INFO @ Mon, 03 Jun 2019 21:07:18: 9000000 INFO @ Mon, 03 Jun 2019 21:07:24: 10000000 INFO @ Mon, 03 Jun 2019 21:07:25: 10000000 INFO @ Mon, 03 Jun 2019 21:07:27: 10000000 INFO @ Mon, 03 Jun 2019 21:07:33: 11000000 INFO @ Mon, 03 Jun 2019 21:07:33: 11000000 INFO @ Mon, 03 Jun 2019 21:07:36: 11000000 INFO @ Mon, 03 Jun 2019 21:07:41: 12000000 INFO @ Mon, 03 Jun 2019 21:07:42: 12000000 INFO @ Mon, 03 Jun 2019 21:07:45: 12000000 INFO @ Mon, 03 Jun 2019 21:07:50: 13000000 INFO @ Mon, 03 Jun 2019 21:07:51: 13000000 INFO @ Mon, 03 Jun 2019 21:07:55: 13000000 INFO @ Mon, 03 Jun 2019 21:07:58: 14000000 INFO @ Mon, 03 Jun 2019 21:07:59: 14000000 INFO @ Mon, 03 Jun 2019 21:08:04: 14000000 INFO @ Mon, 03 Jun 2019 21:08:07: 15000000 INFO @ Mon, 03 Jun 2019 21:08:08: 15000000 INFO @ Mon, 03 Jun 2019 21:08:13: 15000000 INFO @ Mon, 03 Jun 2019 21:08:15: 16000000 INFO @ Mon, 03 Jun 2019 21:08:16: 16000000 INFO @ Mon, 03 Jun 2019 21:08:23: 16000000 INFO @ Mon, 03 Jun 2019 21:08:24: 17000000 INFO @ Mon, 03 Jun 2019 21:08:25: 17000000 INFO @ Mon, 03 Jun 2019 21:08:32: 17000000 INFO @ Mon, 03 Jun 2019 21:08:32: 18000000 INFO @ Mon, 03 Jun 2019 21:08:33: 18000000 INFO @ Mon, 03 Jun 2019 21:08:41: 19000000 INFO @ Mon, 03 Jun 2019 21:08:41: 18000000 INFO @ Mon, 03 Jun 2019 21:08:42: 19000000 INFO @ Mon, 03 Jun 2019 21:08:49: 20000000 INFO @ Mon, 03 Jun 2019 21:08:50: 19000000 INFO @ Mon, 03 Jun 2019 21:08:50: 20000000 INFO @ Mon, 03 Jun 2019 21:08:57: 21000000 INFO @ Mon, 03 Jun 2019 21:08:59: 20000000 INFO @ Mon, 03 Jun 2019 21:08:59: 21000000 INFO @ Mon, 03 Jun 2019 21:09:06: 22000000 INFO @ Mon, 03 Jun 2019 21:09:07: 22000000 INFO @ Mon, 03 Jun 2019 21:09:08: 21000000 INFO @ Mon, 03 Jun 2019 21:09:14: 23000000 INFO @ Mon, 03 Jun 2019 21:09:16: 23000000 INFO @ Mon, 03 Jun 2019 21:09:17: 22000000 INFO @ Mon, 03 Jun 2019 21:09:22: 24000000 INFO @ Mon, 03 Jun 2019 21:09:24: 24000000 INFO @ Mon, 03 Jun 2019 21:09:26: 23000000 INFO @ Mon, 03 Jun 2019 21:09:30: 25000000 INFO @ Mon, 03 Jun 2019 21:09:32: 25000000 INFO @ Mon, 03 Jun 2019 21:09:34: 24000000 INFO @ Mon, 03 Jun 2019 21:09:38: 26000000 INFO @ Mon, 03 Jun 2019 21:09:41: 26000000 INFO @ Mon, 03 Jun 2019 21:09:43: 25000000 INFO @ Mon, 03 Jun 2019 21:09:46: 27000000 INFO @ Mon, 03 Jun 2019 21:09:49: 27000000 INFO @ Mon, 03 Jun 2019 21:09:52: 26000000 INFO @ Mon, 03 Jun 2019 21:09:53: 28000000 INFO @ Mon, 03 Jun 2019 21:09:57: 28000000 INFO @ Mon, 03 Jun 2019 21:10:00: 29000000 INFO @ Mon, 03 Jun 2019 21:10:02: 27000000 INFO @ Mon, 03 Jun 2019 21:10:06: 29000000 INFO @ Mon, 03 Jun 2019 21:10:07: 30000000 INFO @ Mon, 03 Jun 2019 21:10:10: 28000000 INFO @ Mon, 03 Jun 2019 21:10:14: 30000000 INFO @ Mon, 03 Jun 2019 21:10:15: 31000000 INFO @ Mon, 03 Jun 2019 21:10:19: 29000000 INFO @ Mon, 03 Jun 2019 21:10:22: 32000000 INFO @ Mon, 03 Jun 2019 21:10:23: 31000000 INFO @ Mon, 03 Jun 2019 21:10:28: 30000000 INFO @ Mon, 03 Jun 2019 21:10:29: 33000000 INFO @ Mon, 03 Jun 2019 21:10:31: 32000000 INFO @ Mon, 03 Jun 2019 21:10:36: 34000000 INFO @ Mon, 03 Jun 2019 21:10:37: 31000000 INFO @ Mon, 03 Jun 2019 21:10:39: 33000000 INFO @ Mon, 03 Jun 2019 21:10:44: 35000000 INFO @ Mon, 03 Jun 2019 21:10:46: 32000000 INFO @ Mon, 03 Jun 2019 21:10:48: 34000000 INFO @ Mon, 03 Jun 2019 21:10:51: 36000000 INFO @ Mon, 03 Jun 2019 21:10:55: 33000000 INFO @ Mon, 03 Jun 2019 21:10:56: 35000000 INFO @ Mon, 03 Jun 2019 21:10:58: 37000000 INFO @ Mon, 03 Jun 2019 21:11:04: 34000000 INFO @ Mon, 03 Jun 2019 21:11:05: 36000000 INFO @ Mon, 03 Jun 2019 21:11:05: 38000000 INFO @ Mon, 03 Jun 2019 21:11:13: 39000000 INFO @ Mon, 03 Jun 2019 21:11:13: 37000000 INFO @ Mon, 03 Jun 2019 21:11:13: 35000000 INFO @ Mon, 03 Jun 2019 21:11:21: 40000000 INFO @ Mon, 03 Jun 2019 21:11:22: 38000000 INFO @ Mon, 03 Jun 2019 21:11:22: 36000000 INFO @ Mon, 03 Jun 2019 21:11:29: 41000000 INFO @ Mon, 03 Jun 2019 21:11:30: 39000000 INFO @ Mon, 03 Jun 2019 21:11:31: 37000000 INFO @ Mon, 03 Jun 2019 21:11:36: 42000000 INFO @ Mon, 03 Jun 2019 21:11:37: 40000000 INFO @ Mon, 03 Jun 2019 21:11:41: 38000000 INFO @ Mon, 03 Jun 2019 21:11:43: 43000000 INFO @ Mon, 03 Jun 2019 21:11:45: 41000000 INFO @ Mon, 03 Jun 2019 21:11:49: 39000000 INFO @ Mon, 03 Jun 2019 21:11:51: 44000000 INFO @ Mon, 03 Jun 2019 21:11:54: 42000000 INFO @ Mon, 03 Jun 2019 21:11:57: 40000000 INFO @ Mon, 03 Jun 2019 21:11:58: 45000000 INFO @ Mon, 03 Jun 2019 21:12:02: 43000000 INFO @ Mon, 03 Jun 2019 21:12:05: 46000000 INFO @ Mon, 03 Jun 2019 21:12:06: 41000000 INFO @ Mon, 03 Jun 2019 21:12:11: 44000000 INFO @ Mon, 03 Jun 2019 21:12:12: 47000000 INFO @ Mon, 03 Jun 2019 21:12:15: 42000000 INFO @ Mon, 03 Jun 2019 21:12:19: 48000000 INFO @ Mon, 03 Jun 2019 21:12:19: 45000000 INFO @ Mon, 03 Jun 2019 21:12:24: 43000000 INFO @ Mon, 03 Jun 2019 21:12:26: 49000000 INFO @ Mon, 03 Jun 2019 21:12:27: 46000000 INFO @ Mon, 03 Jun 2019 21:12:33: 44000000 INFO @ Mon, 03 Jun 2019 21:12:33: 50000000 INFO @ Mon, 03 Jun 2019 21:12:35: 47000000 INFO @ Mon, 03 Jun 2019 21:12:41: 51000000 INFO @ Mon, 03 Jun 2019 21:12:42: 45000000 INFO @ Mon, 03 Jun 2019 21:12:43: 48000000 INFO @ Mon, 03 Jun 2019 21:12:48: 52000000 INFO @ Mon, 03 Jun 2019 21:12:50: 46000000 INFO @ Mon, 03 Jun 2019 21:12:52: 49000000 INFO @ Mon, 03 Jun 2019 21:12:55: 53000000 INFO @ Mon, 03 Jun 2019 21:12:59: 47000000 INFO @ Mon, 03 Jun 2019 21:13:00: 50000000 INFO @ Mon, 03 Jun 2019 21:13:04: 54000000 INFO @ Mon, 03 Jun 2019 21:13:08: 48000000 INFO @ Mon, 03 Jun 2019 21:13:08: 51000000 INFO @ Mon, 03 Jun 2019 21:13:12: 55000000 INFO @ Mon, 03 Jun 2019 21:13:16: 49000000 INFO @ Mon, 03 Jun 2019 21:13:17: 52000000 INFO @ Mon, 03 Jun 2019 21:13:20: 56000000 INFO @ Mon, 03 Jun 2019 21:13:24: 53000000 INFO @ Mon, 03 Jun 2019 21:13:25: 50000000 INFO @ Mon, 03 Jun 2019 21:13:28: 57000000 INFO @ Mon, 03 Jun 2019 21:13:32: 54000000 INFO @ Mon, 03 Jun 2019 21:13:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:13:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:13:34: #1 total tags in treatment: 27930330 INFO @ Mon, 03 Jun 2019 21:13:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:13:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 21:13:34: 51000000 INFO @ Mon, 03 Jun 2019 21:13:34: #1 tags after filtering in treatment: 25438531 INFO @ Mon, 03 Jun 2019 21:13:34: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 21:13:34: #1 finished! INFO @ Mon, 03 Jun 2019 21:13:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:13:37: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 21:13:37: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 21:13:37: start model_add_line... INFO @ Mon, 03 Jun 2019 21:13:37: start X-correlation... INFO @ Mon, 03 Jun 2019 21:13:37: end of X-cor INFO @ Mon, 03 Jun 2019 21:13:37: #2 finished! INFO @ Mon, 03 Jun 2019 21:13:37: #2 predicted fragment length is 93 bps INFO @ Mon, 03 Jun 2019 21:13:37: #2 alternative fragment length(s) may be 93 bps INFO @ Mon, 03 Jun 2019 21:13:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.10_model.r WARNING @ Mon, 03 Jun 2019 21:13:37: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:13:37: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Mon, 03 Jun 2019 21:13:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 21:13:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:13:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:13:39: 55000000 INFO @ Mon, 03 Jun 2019 21:13:43: 52000000 INFO @ Mon, 03 Jun 2019 21:13:46: 56000000 INFO @ Mon, 03 Jun 2019 21:13:51: 53000000 INFO @ Mon, 03 Jun 2019 21:13:54: 57000000 INFO @ Mon, 03 Jun 2019 21:13:59: 54000000 INFO @ Mon, 03 Jun 2019 21:14:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:14:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:14:02: #1 total tags in treatment: 27930330 INFO @ Mon, 03 Jun 2019 21:14:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:14:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 21:14:02: #1 tags after filtering in treatment: 25438531 INFO @ Mon, 03 Jun 2019 21:14:02: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 21:14:02: #1 finished! INFO @ Mon, 03 Jun 2019 21:14:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:14:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:14:04: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 21:14:04: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 21:14:04: start model_add_line... INFO @ Mon, 03 Jun 2019 21:14:05: start X-correlation... INFO @ Mon, 03 Jun 2019 21:14:05: end of X-cor INFO @ Mon, 03 Jun 2019 21:14:05: #2 finished! INFO @ Mon, 03 Jun 2019 21:14:05: #2 predicted fragment length is 93 bps INFO @ Mon, 03 Jun 2019 21:14:05: #2 alternative fragment length(s) may be 93 bps INFO @ Mon, 03 Jun 2019 21:14:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.20_model.r WARNING @ Mon, 03 Jun 2019 21:14:05: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:14:05: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Mon, 03 Jun 2019 21:14:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 21:14:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:14:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:14:06: 55000000 INFO @ Mon, 03 Jun 2019 21:14:14: 56000000 INFO @ Mon, 03 Jun 2019 21:14:23: 57000000 INFO @ Mon, 03 Jun 2019 21:14:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:14:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:14:31: #1 total tags in treatment: 27930330 INFO @ Mon, 03 Jun 2019 21:14:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:14:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 21:14:31: #1 tags after filtering in treatment: 25438531 INFO @ Mon, 03 Jun 2019 21:14:31: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 21:14:31: #1 finished! INFO @ Mon, 03 Jun 2019 21:14:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:14:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:14:33: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 21:14:33: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 21:14:33: start model_add_line... INFO @ Mon, 03 Jun 2019 21:14:33: start X-correlation... INFO @ Mon, 03 Jun 2019 21:14:33: end of X-cor INFO @ Mon, 03 Jun 2019 21:14:33: #2 finished! INFO @ Mon, 03 Jun 2019 21:14:33: #2 predicted fragment length is 93 bps INFO @ Mon, 03 Jun 2019 21:14:33: #2 alternative fragment length(s) may be 93 bps INFO @ Mon, 03 Jun 2019 21:14:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.05_model.r WARNING @ Mon, 03 Jun 2019 21:14:33: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:14:33: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Mon, 03 Jun 2019 21:14:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 21:14:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:14:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:14:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:15:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:15:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.10_peaks.xls INFO @ Mon, 03 Jun 2019 21:15:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:15:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.10_summits.bed INFO @ Mon, 03 Jun 2019 21:15:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1194 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:15:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.20_peaks.xls INFO @ Mon, 03 Jun 2019 21:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.20_summits.bed INFO @ Mon, 03 Jun 2019 21:15:37: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (848 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.05_peaks.xls INFO @ Mon, 03 Jun 2019 21:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474615/SRX474615.05_summits.bed INFO @ Mon, 03 Jun 2019 21:16:05: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1681 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。