Job ID = 6527404 SRX = SRX2737088 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:21:11 prefetch.2.10.7: 1) Downloading 'SRR5448126'... 2020-06-29T12:21:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:24:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:24:22 prefetch.2.10.7: 1) 'SRR5448126' was downloaded successfully 2020-06-29T12:24:22 prefetch.2.10.7: 'SRR5448126' has 0 unresolved dependencies Read 34451664 spots for SRR5448126/SRR5448126.sra Written 34451664 spots for SRR5448126/SRR5448126.sra 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: 00:07:17 34451664 reads; of these: 34451664 (100.00%) were unpaired; of these: 1617590 (4.70%) aligned 0 times 28142664 (81.69%) aligned exactly 1 time 4691410 (13.62%) aligned >1 times 95.30% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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 16 files... [bam_rmdupse_core] 7211502 / 32834074 = 0.2196 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 @ Mon, 29 Jun 2020 21:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.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 @ Mon, 29 Jun 2020 21:45:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:45:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:45:51: 1000000 INFO @ Mon, 29 Jun 2020 21:45:56: 2000000 INFO @ Mon, 29 Jun 2020 21:46:02: 3000000 INFO @ Mon, 29 Jun 2020 21:46:08: 4000000 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 @ Mon, 29 Jun 2020 21:46:13: 5000000 INFO @ Mon, 29 Jun 2020 21:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.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 @ Mon, 29 Jun 2020 21:46:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:46:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:46:20: 6000000 INFO @ Mon, 29 Jun 2020 21:46:21: 1000000 INFO @ Mon, 29 Jun 2020 21:46:26: 7000000 INFO @ Mon, 29 Jun 2020 21:46:28: 2000000 INFO @ Mon, 29 Jun 2020 21:46:32: 8000000 INFO @ Mon, 29 Jun 2020 21:46:34: 3000000 INFO @ Mon, 29 Jun 2020 21:46:39: 9000000 INFO @ Mon, 29 Jun 2020 21:46:41: 4000000 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 @ Mon, 29 Jun 2020 21:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.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 @ Mon, 29 Jun 2020 21:46:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:46:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:46:45: 10000000 INFO @ Mon, 29 Jun 2020 21:46:47: 5000000 INFO @ Mon, 29 Jun 2020 21:46:51: 1000000 INFO @ Mon, 29 Jun 2020 21:46:52: 11000000 INFO @ Mon, 29 Jun 2020 21:46:54: 6000000 INFO @ Mon, 29 Jun 2020 21:46:58: 2000000 INFO @ Mon, 29 Jun 2020 21:46:58: 12000000 INFO @ Mon, 29 Jun 2020 21:47:00: 7000000 INFO @ Mon, 29 Jun 2020 21:47:04: 3000000 INFO @ Mon, 29 Jun 2020 21:47:05: 13000000 INFO @ Mon, 29 Jun 2020 21:47:07: 8000000 INFO @ Mon, 29 Jun 2020 21:47:11: 4000000 INFO @ Mon, 29 Jun 2020 21:47:11: 14000000 INFO @ Mon, 29 Jun 2020 21:47:13: 9000000 INFO @ Mon, 29 Jun 2020 21:47:18: 5000000 INFO @ Mon, 29 Jun 2020 21:47:18: 15000000 INFO @ Mon, 29 Jun 2020 21:47:20: 10000000 INFO @ Mon, 29 Jun 2020 21:47:24: 6000000 INFO @ Mon, 29 Jun 2020 21:47:25: 16000000 INFO @ Mon, 29 Jun 2020 21:47:27: 11000000 INFO @ Mon, 29 Jun 2020 21:47:31: 7000000 INFO @ Mon, 29 Jun 2020 21:47:31: 17000000 INFO @ Mon, 29 Jun 2020 21:47:33: 12000000 INFO @ Mon, 29 Jun 2020 21:47:37: 8000000 INFO @ Mon, 29 Jun 2020 21:47:38: 18000000 INFO @ Mon, 29 Jun 2020 21:47:40: 13000000 INFO @ Mon, 29 Jun 2020 21:47:44: 9000000 INFO @ Mon, 29 Jun 2020 21:47:45: 19000000 INFO @ Mon, 29 Jun 2020 21:47:47: 14000000 INFO @ Mon, 29 Jun 2020 21:47:51: 10000000 INFO @ Mon, 29 Jun 2020 21:47:51: 20000000 INFO @ Mon, 29 Jun 2020 21:47:53: 15000000 INFO @ Mon, 29 Jun 2020 21:47:57: 11000000 INFO @ Mon, 29 Jun 2020 21:47:58: 21000000 INFO @ Mon, 29 Jun 2020 21:48:00: 16000000 INFO @ Mon, 29 Jun 2020 21:48:04: 12000000 INFO @ Mon, 29 Jun 2020 21:48:05: 22000000 INFO @ Mon, 29 Jun 2020 21:48:07: 17000000 INFO @ Mon, 29 Jun 2020 21:48:10: 13000000 INFO @ Mon, 29 Jun 2020 21:48:12: 23000000 INFO @ Mon, 29 Jun 2020 21:48:13: 18000000 INFO @ Mon, 29 Jun 2020 21:48:17: 14000000 INFO @ Mon, 29 Jun 2020 21:48:18: 24000000 INFO @ Mon, 29 Jun 2020 21:48:20: 19000000 INFO @ Mon, 29 Jun 2020 21:48:24: 15000000 INFO @ Mon, 29 Jun 2020 21:48:25: 25000000 INFO @ Mon, 29 Jun 2020 21:48:27: 20000000 INFO @ Mon, 29 Jun 2020 21:48:30: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 21:48:30: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 21:48:30: #1 total tags in treatment: 25622572 INFO @ Mon, 29 Jun 2020 21:48:30: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:48:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:48:30: #1 tags after filtering in treatment: 25622572 INFO @ Mon, 29 Jun 2020 21:48:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:48:30: #1 finished! INFO @ Mon, 29 Jun 2020 21:48:30: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:48:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:48:31: 16000000 INFO @ Mon, 29 Jun 2020 21:48:32: #2 number of paired peaks: 121 WARNING @ Mon, 29 Jun 2020 21:48:32: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 29 Jun 2020 21:48:32: start model_add_line... INFO @ Mon, 29 Jun 2020 21:48:32: start X-correlation... INFO @ Mon, 29 Jun 2020 21:48:32: end of X-cor INFO @ Mon, 29 Jun 2020 21:48:32: #2 finished! INFO @ Mon, 29 Jun 2020 21:48:32: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 21:48:32: #2 alternative fragment length(s) may be 44,491,508,528,540 bps INFO @ Mon, 29 Jun 2020 21:48:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.05_model.r WARNING @ Mon, 29 Jun 2020 21:48:32: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:48:32: #2 You may need to consider one of the other alternative d(s): 44,491,508,528,540 WARNING @ Mon, 29 Jun 2020 21:48:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:48:32: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:48:32: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:48:34: 21000000 INFO @ Mon, 29 Jun 2020 21:48:38: 17000000 INFO @ Mon, 29 Jun 2020 21:48:42: 22000000 INFO @ Mon, 29 Jun 2020 21:48:45: 18000000 INFO @ Mon, 29 Jun 2020 21:48:49: 23000000 INFO @ Mon, 29 Jun 2020 21:48:52: 19000000 INFO @ Mon, 29 Jun 2020 21:48:56: 24000000 INFO @ Mon, 29 Jun 2020 21:48:59: 20000000 INFO @ Mon, 29 Jun 2020 21:49:03: 25000000 INFO @ Mon, 29 Jun 2020 21:49:06: 21000000 INFO @ Mon, 29 Jun 2020 21:49:07: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 21:49:07: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 21:49:07: #1 total tags in treatment: 25622572 INFO @ Mon, 29 Jun 2020 21:49:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:49:07: #1 tags after filtering in treatment: 25622572 INFO @ Mon, 29 Jun 2020 21:49:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:07: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:07: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:09: #2 number of paired peaks: 121 WARNING @ Mon, 29 Jun 2020 21:49:09: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 29 Jun 2020 21:49:09: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:09: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:09: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:09: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:09: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 21:49:09: #2 alternative fragment length(s) may be 44,491,508,528,540 bps INFO @ Mon, 29 Jun 2020 21:49:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.10_model.r WARNING @ Mon, 29 Jun 2020 21:49:09: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:09: #2 You may need to consider one of the other alternative d(s): 44,491,508,528,540 WARNING @ Mon, 29 Jun 2020 21:49:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:49:09: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:49:13: 22000000 INFO @ Mon, 29 Jun 2020 21:49:14: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:49:19: 23000000 INFO @ Mon, 29 Jun 2020 21:49:25: 24000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 21:49:32: 25000000 INFO @ Mon, 29 Jun 2020 21:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.05_summits.bed INFO @ Mon, 29 Jun 2020 21:49:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (722 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:49:35: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 21:49:35: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 21:49:35: #1 total tags in treatment: 25622572 INFO @ Mon, 29 Jun 2020 21:49:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:49:36: #1 tags after filtering in treatment: 25622572 INFO @ Mon, 29 Jun 2020 21:49:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:36: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:36: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:37: #2 number of paired peaks: 121 WARNING @ Mon, 29 Jun 2020 21:49:37: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 29 Jun 2020 21:49:37: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:38: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:38: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:38: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:38: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 21:49:38: #2 alternative fragment length(s) may be 44,491,508,528,540 bps INFO @ Mon, 29 Jun 2020 21:49:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.20_model.r WARNING @ Mon, 29 Jun 2020 21:49:38: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:38: #2 You may need to consider one of the other alternative d(s): 44,491,508,528,540 WARNING @ Mon, 29 Jun 2020 21:49:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:49:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:49:50: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:50:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:50:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:50:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.10_summits.bed INFO @ Mon, 29 Jun 2020 21:50:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:50:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:50:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:50:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:50:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737088/SRX2737088.20_summits.bed INFO @ Mon, 29 Jun 2020 21:50:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 1 millis CompletedMACS2peakCalling