Job ID = 5720194 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T12:49:34 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 ) 2020-04-15T12:51:12 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 ) 2020-04-15T12:51:12 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 ) 2020-04-15T12:52:03 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 ) 2020-04-15T12:52:03 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 ) 2020-04-15T12:54:16 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 ) 2020-04-15T12:54:27 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 ) 2020-04-15T13:02:55 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 ) 2020-04-15T13:12:00 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 ) 2020-04-15T13:18:33 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 ) 2020-04-15T13:29:22 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 : 36,677,495 reads read : 73,354,990 reads written : 73,354,990 rm: cannot remove ‘[DSE]RR*’: 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: 01:12:11 36677495 reads; of these: 36677495 (100.00%) were paired; of these: 16195801 (44.16%) aligned concordantly 0 times 17417395 (47.49%) aligned concordantly exactly 1 time 3064299 (8.35%) aligned concordantly >1 times ---- 16195801 pairs aligned concordantly 0 times; of these: 9762016 (60.27%) aligned discordantly 1 time ---- 6433785 pairs aligned 0 times concordantly or discordantly; of these: 12867570 mates make up the pairs; of these: 9331879 (72.52%) aligned 0 times 1761464 (13.69%) aligned exactly 1 time 1774227 (13.79%) aligned >1 times 87.28% overall alignment rate Time searching: 01:12:12 Overall time: 01:12:12 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 48 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] 4900617 / 29419022 = 0.1666 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 00:10:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.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 @ Thu, 16 Apr 2020 00:10:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:10:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:10:52: 1000000 INFO @ Thu, 16 Apr 2020 00:10:59: 2000000 INFO @ Thu, 16 Apr 2020 00:11:06: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 00:11:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.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 @ Thu, 16 Apr 2020 00:11:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:11:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:11:14: 4000000 INFO @ Thu, 16 Apr 2020 00:11:22: 1000000 INFO @ Thu, 16 Apr 2020 00:11:22: 5000000 INFO @ Thu, 16 Apr 2020 00:11:29: 2000000 INFO @ Thu, 16 Apr 2020 00:11:30: 6000000 INFO @ Thu, 16 Apr 2020 00:11:37: 3000000 INFO @ Thu, 16 Apr 2020 00:11:37: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 00:11:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.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 @ Thu, 16 Apr 2020 00:11:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:11:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:11:45: 8000000 INFO @ Thu, 16 Apr 2020 00:11:46: 4000000 INFO @ Thu, 16 Apr 2020 00:11:52: 1000000 INFO @ Thu, 16 Apr 2020 00:11:53: 9000000 INFO @ Thu, 16 Apr 2020 00:11:54: 5000000 INFO @ Thu, 16 Apr 2020 00:12:00: 2000000 INFO @ Thu, 16 Apr 2020 00:12:02: 10000000 INFO @ Thu, 16 Apr 2020 00:12:02: 6000000 INFO @ Thu, 16 Apr 2020 00:12:08: 3000000 INFO @ Thu, 16 Apr 2020 00:12:11: 7000000 INFO @ Thu, 16 Apr 2020 00:12:11: 11000000 INFO @ Thu, 16 Apr 2020 00:12:17: 4000000 INFO @ Thu, 16 Apr 2020 00:12:19: 8000000 INFO @ Thu, 16 Apr 2020 00:12:21: 12000000 INFO @ Thu, 16 Apr 2020 00:12:26: 5000000 INFO @ Thu, 16 Apr 2020 00:12:27: 9000000 INFO @ Thu, 16 Apr 2020 00:12:31: 13000000 INFO @ Thu, 16 Apr 2020 00:12:34: 6000000 INFO @ Thu, 16 Apr 2020 00:12:36: 10000000 INFO @ Thu, 16 Apr 2020 00:12:41: 14000000 INFO @ Thu, 16 Apr 2020 00:12:43: 7000000 INFO @ Thu, 16 Apr 2020 00:12:44: 11000000 INFO @ Thu, 16 Apr 2020 00:12:52: 15000000 INFO @ Thu, 16 Apr 2020 00:12:52: 8000000 INFO @ Thu, 16 Apr 2020 00:12:54: 12000000 INFO @ Thu, 16 Apr 2020 00:13:02: 16000000 INFO @ Thu, 16 Apr 2020 00:13:02: 13000000 INFO @ Thu, 16 Apr 2020 00:13:04: 9000000 INFO @ Thu, 16 Apr 2020 00:13:11: 14000000 INFO @ Thu, 16 Apr 2020 00:13:12: 17000000 INFO @ Thu, 16 Apr 2020 00:13:13: 10000000 INFO @ Thu, 16 Apr 2020 00:13:19: 15000000 INFO @ Thu, 16 Apr 2020 00:13:23: 18000000 INFO @ Thu, 16 Apr 2020 00:13:23: 11000000 INFO @ Thu, 16 Apr 2020 00:13:28: 16000000 INFO @ Thu, 16 Apr 2020 00:13:33: 19000000 INFO @ Thu, 16 Apr 2020 00:13:34: 12000000 INFO @ Thu, 16 Apr 2020 00:13:37: 17000000 INFO @ Thu, 16 Apr 2020 00:13:42: 13000000 INFO @ Thu, 16 Apr 2020 00:13:44: 20000000 INFO @ Thu, 16 Apr 2020 00:13:45: 18000000 INFO @ Thu, 16 Apr 2020 00:13:50: 14000000 INFO @ Thu, 16 Apr 2020 00:13:53: 19000000 INFO @ Thu, 16 Apr 2020 00:13:54: 21000000 INFO @ Thu, 16 Apr 2020 00:13:59: 15000000 INFO @ Thu, 16 Apr 2020 00:14:01: 20000000 INFO @ Thu, 16 Apr 2020 00:14:04: 22000000 INFO @ Thu, 16 Apr 2020 00:14:09: 16000000 INFO @ Thu, 16 Apr 2020 00:14:09: 21000000 INFO @ Thu, 16 Apr 2020 00:14:15: 23000000 INFO @ Thu, 16 Apr 2020 00:14:18: 22000000 INFO @ Thu, 16 Apr 2020 00:14:18: 17000000 INFO @ Thu, 16 Apr 2020 00:14:25: 24000000 INFO @ Thu, 16 Apr 2020 00:14:26: 23000000 INFO @ Thu, 16 Apr 2020 00:14:28: 18000000 INFO @ Thu, 16 Apr 2020 00:14:35: 24000000 INFO @ Thu, 16 Apr 2020 00:14:35: 25000000 INFO @ Thu, 16 Apr 2020 00:14:38: 19000000 INFO @ Thu, 16 Apr 2020 00:14:43: 25000000 INFO @ Thu, 16 Apr 2020 00:14:46: 26000000 INFO @ Thu, 16 Apr 2020 00:14:47: 20000000 INFO @ Thu, 16 Apr 2020 00:14:52: 26000000 INFO @ Thu, 16 Apr 2020 00:14:55: 27000000 INFO @ Thu, 16 Apr 2020 00:14:57: 21000000 INFO @ Thu, 16 Apr 2020 00:15:00: 27000000 INFO @ Thu, 16 Apr 2020 00:15:05: 28000000 INFO @ Thu, 16 Apr 2020 00:15:08: 22000000 INFO @ Thu, 16 Apr 2020 00:15:09: 28000000 INFO @ Thu, 16 Apr 2020 00:15:15: 29000000 INFO @ Thu, 16 Apr 2020 00:15:18: 23000000 INFO @ Thu, 16 Apr 2020 00:15:18: 29000000 INFO @ Thu, 16 Apr 2020 00:15:25: 30000000 INFO @ Thu, 16 Apr 2020 00:15:27: 30000000 INFO @ Thu, 16 Apr 2020 00:15:27: 24000000 INFO @ Thu, 16 Apr 2020 00:15:36: 25000000 INFO @ Thu, 16 Apr 2020 00:15:36: 31000000 INFO @ Thu, 16 Apr 2020 00:15:40: 31000000 INFO @ Thu, 16 Apr 2020 00:15:44: 26000000 INFO @ Thu, 16 Apr 2020 00:15:44: 32000000 INFO @ Thu, 16 Apr 2020 00:15:52: 33000000 INFO @ Thu, 16 Apr 2020 00:15:52: 27000000 INFO @ Thu, 16 Apr 2020 00:15:55: 32000000 INFO @ Thu, 16 Apr 2020 00:16:01: 34000000 INFO @ Thu, 16 Apr 2020 00:16:03: 28000000 INFO @ Thu, 16 Apr 2020 00:16:09: 33000000 INFO @ Thu, 16 Apr 2020 00:16:10: 35000000 INFO @ Thu, 16 Apr 2020 00:16:14: 29000000 INFO @ Thu, 16 Apr 2020 00:16:18: 36000000 INFO @ Thu, 16 Apr 2020 00:16:23: 30000000 INFO @ Thu, 16 Apr 2020 00:16:24: 34000000 INFO @ Thu, 16 Apr 2020 00:16:27: 37000000 INFO @ Thu, 16 Apr 2020 00:16:34: 31000000 INFO @ Thu, 16 Apr 2020 00:16:35: 38000000 INFO @ Thu, 16 Apr 2020 00:16:39: 35000000 INFO @ Thu, 16 Apr 2020 00:16:44: 39000000 INFO @ Thu, 16 Apr 2020 00:16:46: 32000000 INFO @ Thu, 16 Apr 2020 00:16:53: 40000000 INFO @ Thu, 16 Apr 2020 00:16:56: 33000000 INFO @ Thu, 16 Apr 2020 00:16:56: 36000000 INFO @ Thu, 16 Apr 2020 00:17:02: 41000000 INFO @ Thu, 16 Apr 2020 00:17:06: 34000000 INFO @ Thu, 16 Apr 2020 00:17:10: 42000000 INFO @ Thu, 16 Apr 2020 00:17:11: 37000000 INFO @ Thu, 16 Apr 2020 00:17:16: 35000000 INFO @ Thu, 16 Apr 2020 00:17:19: 43000000 INFO @ Thu, 16 Apr 2020 00:17:23: 38000000 INFO @ Thu, 16 Apr 2020 00:17:26: 36000000 INFO @ Thu, 16 Apr 2020 00:17:27: 44000000 INFO @ Thu, 16 Apr 2020 00:17:35: 39000000 INFO @ Thu, 16 Apr 2020 00:17:35: 37000000 INFO @ Thu, 16 Apr 2020 00:17:36: 45000000 INFO @ Thu, 16 Apr 2020 00:17:45: 46000000 INFO @ Thu, 16 Apr 2020 00:17:45: 38000000 INFO @ Thu, 16 Apr 2020 00:17:47: 40000000 INFO @ Thu, 16 Apr 2020 00:17:53: 47000000 INFO @ Thu, 16 Apr 2020 00:17:55: 39000000 INFO @ Thu, 16 Apr 2020 00:18:01: 48000000 INFO @ Thu, 16 Apr 2020 00:18:01: 41000000 INFO @ Thu, 16 Apr 2020 00:18:04: 40000000 INFO @ Thu, 16 Apr 2020 00:18:10: 49000000 INFO @ Thu, 16 Apr 2020 00:18:14: 41000000 INFO @ Thu, 16 Apr 2020 00:18:14: 42000000 INFO @ Thu, 16 Apr 2020 00:18:18: 50000000 INFO @ Thu, 16 Apr 2020 00:18:24: 42000000 INFO @ Thu, 16 Apr 2020 00:18:25: 43000000 INFO @ Thu, 16 Apr 2020 00:18:27: 51000000 INFO @ Thu, 16 Apr 2020 00:18:32: 43000000 INFO @ Thu, 16 Apr 2020 00:18:35: 44000000 INFO @ Thu, 16 Apr 2020 00:18:36: 52000000 INFO @ Thu, 16 Apr 2020 00:18:42: 44000000 INFO @ Thu, 16 Apr 2020 00:18:45: 53000000 INFO @ Thu, 16 Apr 2020 00:18:46: 45000000 INFO @ Thu, 16 Apr 2020 00:18:52: 45000000 INFO @ Thu, 16 Apr 2020 00:18:53: 54000000 INFO @ Thu, 16 Apr 2020 00:18:55: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 00:18:55: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 00:18:55: #1 total tags in treatment: 16953620 INFO @ Thu, 16 Apr 2020 00:18:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:18:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:18:55: #1 tags after filtering in treatment: 14469228 INFO @ Thu, 16 Apr 2020 00:18:55: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 00:18:55: #1 finished! INFO @ Thu, 16 Apr 2020 00:18:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:18:56: 46000000 INFO @ Thu, 16 Apr 2020 00:18:56: #2 number of paired peaks: 237 WARNING @ Thu, 16 Apr 2020 00:18:56: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Thu, 16 Apr 2020 00:18:56: start model_add_line... INFO @ Thu, 16 Apr 2020 00:18:56: start X-correlation... INFO @ Thu, 16 Apr 2020 00:18:56: end of X-cor INFO @ Thu, 16 Apr 2020 00:18:56: #2 finished! INFO @ Thu, 16 Apr 2020 00:18:56: #2 predicted fragment length is 203 bps INFO @ Thu, 16 Apr 2020 00:18:56: #2 alternative fragment length(s) may be 4,203 bps INFO @ Thu, 16 Apr 2020 00:18:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.10_model.r WARNING @ Thu, 16 Apr 2020 00:18:56: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:18:56: #2 You may need to consider one of the other alternative d(s): 4,203 WARNING @ Thu, 16 Apr 2020 00:18:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:18:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:18:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:19:00: 46000000 INFO @ Thu, 16 Apr 2020 00:19:06: 47000000 INFO @ Thu, 16 Apr 2020 00:19:10: 47000000 INFO @ Thu, 16 Apr 2020 00:19:19: 48000000 INFO @ Thu, 16 Apr 2020 00:19:19: 48000000 INFO @ Thu, 16 Apr 2020 00:19:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:19:30: 49000000 INFO @ Thu, 16 Apr 2020 00:19:33: 49000000 INFO @ Thu, 16 Apr 2020 00:19:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:19:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:19:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.10_summits.bed INFO @ Thu, 16 Apr 2020 00:19:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (325 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:19:41: 50000000 INFO @ Thu, 16 Apr 2020 00:19:46: 50000000 INFO @ Thu, 16 Apr 2020 00:19:53: 51000000 INFO @ Thu, 16 Apr 2020 00:19:59: 51000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:20:06: 52000000 INFO @ Thu, 16 Apr 2020 00:20:12: 52000000 INFO @ Thu, 16 Apr 2020 00:20:17: 53000000 INFO @ Thu, 16 Apr 2020 00:20:26: 53000000 INFO @ Thu, 16 Apr 2020 00:20:28: 54000000 INFO @ Thu, 16 Apr 2020 00:20:30: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 00:20:30: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 00:20:30: #1 total tags in treatment: 16953620 INFO @ Thu, 16 Apr 2020 00:20:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:20:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:20:31: #1 tags after filtering in treatment: 14469228 INFO @ Thu, 16 Apr 2020 00:20:31: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 00:20:31: #1 finished! INFO @ Thu, 16 Apr 2020 00:20:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:20:32: #2 number of paired peaks: 237 WARNING @ Thu, 16 Apr 2020 00:20:32: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Thu, 16 Apr 2020 00:20:32: start model_add_line... INFO @ Thu, 16 Apr 2020 00:20:32: start X-correlation... INFO @ Thu, 16 Apr 2020 00:20:32: end of X-cor INFO @ Thu, 16 Apr 2020 00:20:32: #2 finished! INFO @ Thu, 16 Apr 2020 00:20:32: #2 predicted fragment length is 203 bps INFO @ Thu, 16 Apr 2020 00:20:32: #2 alternative fragment length(s) may be 4,203 bps INFO @ Thu, 16 Apr 2020 00:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.20_model.r WARNING @ Thu, 16 Apr 2020 00:20:32: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:20:32: #2 You may need to consider one of the other alternative d(s): 4,203 WARNING @ Thu, 16 Apr 2020 00:20:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:20:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:20:39: 54000000 INFO @ Thu, 16 Apr 2020 00:20:42: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 00:20:42: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 00:20:42: #1 total tags in treatment: 16953620 INFO @ Thu, 16 Apr 2020 00:20:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:20:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:20:43: #1 tags after filtering in treatment: 14469228 INFO @ Thu, 16 Apr 2020 00:20:43: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 00:20:43: #1 finished! INFO @ Thu, 16 Apr 2020 00:20:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:20:43: #2 number of paired peaks: 237 WARNING @ Thu, 16 Apr 2020 00:20:43: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Thu, 16 Apr 2020 00:20:43: start model_add_line... INFO @ Thu, 16 Apr 2020 00:20:44: start X-correlation... INFO @ Thu, 16 Apr 2020 00:20:44: end of X-cor INFO @ Thu, 16 Apr 2020 00:20:44: #2 finished! INFO @ Thu, 16 Apr 2020 00:20:44: #2 predicted fragment length is 203 bps INFO @ Thu, 16 Apr 2020 00:20:44: #2 alternative fragment length(s) may be 4,203 bps INFO @ Thu, 16 Apr 2020 00:20:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.05_model.r WARNING @ Thu, 16 Apr 2020 00:20:44: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:20:44: #2 You may need to consider one of the other alternative d(s): 4,203 WARNING @ Thu, 16 Apr 2020 00:20:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:20:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:21:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:21:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:21:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:21:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:21:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.20_summits.bed INFO @ Thu, 16 Apr 2020 00:21:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (223 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 16 Apr 2020 00:21:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:21:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:21:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619564/SRX6619564.05_summits.bed INFO @ Thu, 16 Apr 2020 00:21:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 1 millis CompletedMACS2peakCalling