Job ID = 6368649 SRX = SRX529209 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:08 prefetch.2.10.7: 1) Downloading 'SRR1265813'... 2020-06-16T00:24:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:26 prefetch.2.10.7: 1) 'SRR1265813' was downloaded successfully Read 20333805 spots for SRR1265813/SRR1265813.sra Written 20333805 spots for SRR1265813/SRR1265813.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: 00:03:46 20333805 reads; of these: 20333805 (100.00%) were unpaired; of these: 242056 (1.19%) aligned 0 times 16212311 (79.73%) aligned exactly 1 time 3879438 (19.08%) aligned >1 times 98.81% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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 8 files... [bam_rmdupse_core] 2866959 / 20091749 = 0.1427 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 @ Tue, 16 Jun 2020 09:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.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 @ Tue, 16 Jun 2020 09:36:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:27: 1000000 INFO @ Tue, 16 Jun 2020 09:36:33: 2000000 INFO @ Tue, 16 Jun 2020 09:36:39: 3000000 INFO @ Tue, 16 Jun 2020 09:36:45: 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 @ Tue, 16 Jun 2020 09:36:51: 5000000 INFO @ Tue, 16 Jun 2020 09:36:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.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 @ Tue, 16 Jun 2020 09:36:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:57: 6000000 INFO @ Tue, 16 Jun 2020 09:36:58: 1000000 INFO @ Tue, 16 Jun 2020 09:37:03: 7000000 INFO @ Tue, 16 Jun 2020 09:37:04: 2000000 INFO @ Tue, 16 Jun 2020 09:37:10: 8000000 INFO @ Tue, 16 Jun 2020 09:37:10: 3000000 INFO @ Tue, 16 Jun 2020 09:37:16: 9000000 INFO @ Tue, 16 Jun 2020 09:37:17: 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 @ Tue, 16 Jun 2020 09:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.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 @ Tue, 16 Jun 2020 09:37:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:22: 10000000 INFO @ Tue, 16 Jun 2020 09:37:23: 5000000 INFO @ Tue, 16 Jun 2020 09:37:28: 1000000 INFO @ Tue, 16 Jun 2020 09:37:29: 11000000 INFO @ Tue, 16 Jun 2020 09:37:29: 6000000 INFO @ Tue, 16 Jun 2020 09:37:35: 2000000 INFO @ Tue, 16 Jun 2020 09:37:35: 12000000 INFO @ Tue, 16 Jun 2020 09:37:35: 7000000 INFO @ Tue, 16 Jun 2020 09:37:41: 3000000 INFO @ Tue, 16 Jun 2020 09:37:41: 13000000 INFO @ Tue, 16 Jun 2020 09:37:42: 8000000 INFO @ Tue, 16 Jun 2020 09:37:48: 4000000 INFO @ Tue, 16 Jun 2020 09:37:48: 14000000 INFO @ Tue, 16 Jun 2020 09:37:48: 9000000 INFO @ Tue, 16 Jun 2020 09:37:54: 5000000 INFO @ Tue, 16 Jun 2020 09:37:54: 15000000 INFO @ Tue, 16 Jun 2020 09:37:55: 10000000 INFO @ Tue, 16 Jun 2020 09:38:01: 6000000 INFO @ Tue, 16 Jun 2020 09:38:01: 16000000 INFO @ Tue, 16 Jun 2020 09:38:01: 11000000 INFO @ Tue, 16 Jun 2020 09:38:07: 7000000 INFO @ Tue, 16 Jun 2020 09:38:07: 17000000 INFO @ Tue, 16 Jun 2020 09:38:07: 12000000 INFO @ Tue, 16 Jun 2020 09:38:08: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:38:08: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:38:08: #1 total tags in treatment: 17224790 INFO @ Tue, 16 Jun 2020 09:38:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:38:09: #1 tags after filtering in treatment: 17224790 INFO @ Tue, 16 Jun 2020 09:38:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:10: #2 number of paired peaks: 209 WARNING @ Tue, 16 Jun 2020 09:38:10: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:10: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:38:10: #2 alternative fragment length(s) may be 2,15,37,489,515,538,574 bps INFO @ Tue, 16 Jun 2020 09:38:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.05_model.r WARNING @ Tue, 16 Jun 2020 09:38:10: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:10: #2 You may need to consider one of the other alternative d(s): 2,15,37,489,515,538,574 WARNING @ Tue, 16 Jun 2020 09:38:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:38:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:13: 8000000 INFO @ Tue, 16 Jun 2020 09:38:14: 13000000 INFO @ Tue, 16 Jun 2020 09:38:20: 9000000 INFO @ Tue, 16 Jun 2020 09:38:20: 14000000 INFO @ Tue, 16 Jun 2020 09:38:26: 15000000 INFO @ Tue, 16 Jun 2020 09:38:26: 10000000 INFO @ Tue, 16 Jun 2020 09:38:32: 16000000 INFO @ Tue, 16 Jun 2020 09:38:33: 11000000 INFO @ Tue, 16 Jun 2020 09:38:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:39: 17000000 INFO @ Tue, 16 Jun 2020 09:38:39: 12000000 INFO @ Tue, 16 Jun 2020 09:38:40: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:38:40: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:38:40: #1 total tags in treatment: 17224790 INFO @ Tue, 16 Jun 2020 09:38:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:38:40: #1 tags after filtering in treatment: 17224790 INFO @ Tue, 16 Jun 2020 09:38:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:41: #2 number of paired peaks: 209 WARNING @ Tue, 16 Jun 2020 09:38:41: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:41: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:38:41: #2 alternative fragment length(s) may be 2,15,37,489,515,538,574 bps INFO @ Tue, 16 Jun 2020 09:38:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.10_model.r WARNING @ Tue, 16 Jun 2020 09:38:41: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:41: #2 You may need to consider one of the other alternative d(s): 2,15,37,489,515,538,574 WARNING @ Tue, 16 Jun 2020 09:38:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:38:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:38:45: 13000000 INFO @ Tue, 16 Jun 2020 09:38:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.05_summits.bed INFO @ Tue, 16 Jun 2020 09:38:48: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:51: 14000000 INFO @ Tue, 16 Jun 2020 09:38:57: 15000000 INFO @ Tue, 16 Jun 2020 09:39:03: 16000000 INFO @ Tue, 16 Jun 2020 09:39:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:09: 17000000 INFO @ Tue, 16 Jun 2020 09:39:11: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:39:11: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:39:11: #1 total tags in treatment: 17224790 INFO @ Tue, 16 Jun 2020 09:39:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:39:11: #1 tags after filtering in treatment: 17224790 INFO @ Tue, 16 Jun 2020 09:39:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:12: #2 number of paired peaks: 209 WARNING @ Tue, 16 Jun 2020 09:39:12: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:12: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:39:12: #2 alternative fragment length(s) may be 2,15,37,489,515,538,574 bps INFO @ Tue, 16 Jun 2020 09:39:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.20_model.r WARNING @ Tue, 16 Jun 2020 09:39:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:39:12: #2 You may need to consider one of the other alternative d(s): 2,15,37,489,515,538,574 WARNING @ Tue, 16 Jun 2020 09:39:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:39:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:39:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.10_summits.bed INFO @ Tue, 16 Jun 2020 09:39:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:39:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529209/SRX529209.20_summits.bed INFO @ Tue, 16 Jun 2020 09:39:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling