Job ID = 6366088 SRX = SRX059266 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:28:14 prefetch.2.10.7: 1) Downloading 'SRR190706'... 2020-06-15T22:28:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:30:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:30:16 prefetch.2.10.7: 1) 'SRR190706' was downloaded successfully Read 37296098 spots for SRR190706/SRR190706.sra Written 37296098 spots for SRR190706/SRR190706.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: 00:06:07 37296098 reads; of these: 37296098 (100.00%) were unpaired; of these: 5738562 (15.39%) aligned 0 times 25918617 (69.49%) aligned exactly 1 time 5638919 (15.12%) aligned >1 times 84.61% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 4251770 / 31557536 = 0.1347 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 07:43:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.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 07:43:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:48: 1000000 INFO @ Tue, 16 Jun 2020 07:43:54: 2000000 INFO @ Tue, 16 Jun 2020 07:44:00: 3000000 INFO @ Tue, 16 Jun 2020 07:44:06: 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 07:44:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.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 07:44:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:12: 5000000 INFO @ Tue, 16 Jun 2020 07:44:17: 1000000 INFO @ Tue, 16 Jun 2020 07:44:19: 6000000 INFO @ Tue, 16 Jun 2020 07:44:24: 2000000 INFO @ Tue, 16 Jun 2020 07:44:25: 7000000 INFO @ Tue, 16 Jun 2020 07:44:30: 3000000 INFO @ Tue, 16 Jun 2020 07:44:32: 8000000 INFO @ Tue, 16 Jun 2020 07:44:36: 4000000 INFO @ Tue, 16 Jun 2020 07:44:39: 9000000 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 07:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.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 07:44:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:42: 5000000 INFO @ Tue, 16 Jun 2020 07:44:46: 10000000 INFO @ Tue, 16 Jun 2020 07:44:48: 1000000 INFO @ Tue, 16 Jun 2020 07:44:49: 6000000 INFO @ Tue, 16 Jun 2020 07:44:52: 11000000 INFO @ Tue, 16 Jun 2020 07:44:54: 2000000 INFO @ Tue, 16 Jun 2020 07:44:55: 7000000 INFO @ Tue, 16 Jun 2020 07:44:59: 12000000 INFO @ Tue, 16 Jun 2020 07:45:01: 3000000 INFO @ Tue, 16 Jun 2020 07:45:02: 8000000 INFO @ Tue, 16 Jun 2020 07:45:06: 13000000 INFO @ Tue, 16 Jun 2020 07:45:07: 4000000 INFO @ Tue, 16 Jun 2020 07:45:08: 9000000 INFO @ Tue, 16 Jun 2020 07:45:13: 14000000 INFO @ Tue, 16 Jun 2020 07:45:14: 5000000 INFO @ Tue, 16 Jun 2020 07:45:14: 10000000 INFO @ Tue, 16 Jun 2020 07:45:20: 15000000 INFO @ Tue, 16 Jun 2020 07:45:20: 6000000 INFO @ Tue, 16 Jun 2020 07:45:21: 11000000 INFO @ Tue, 16 Jun 2020 07:45:26: 7000000 INFO @ Tue, 16 Jun 2020 07:45:27: 16000000 INFO @ Tue, 16 Jun 2020 07:45:27: 12000000 INFO @ Tue, 16 Jun 2020 07:45:33: 8000000 INFO @ Tue, 16 Jun 2020 07:45:33: 13000000 INFO @ Tue, 16 Jun 2020 07:45:34: 17000000 INFO @ Tue, 16 Jun 2020 07:45:39: 9000000 INFO @ Tue, 16 Jun 2020 07:45:40: 14000000 INFO @ Tue, 16 Jun 2020 07:45:41: 18000000 INFO @ Tue, 16 Jun 2020 07:45:46: 10000000 INFO @ Tue, 16 Jun 2020 07:45:46: 15000000 INFO @ Tue, 16 Jun 2020 07:45:48: 19000000 INFO @ Tue, 16 Jun 2020 07:45:52: 11000000 INFO @ Tue, 16 Jun 2020 07:45:53: 16000000 INFO @ Tue, 16 Jun 2020 07:45:55: 20000000 INFO @ Tue, 16 Jun 2020 07:45:59: 12000000 INFO @ Tue, 16 Jun 2020 07:45:59: 17000000 INFO @ Tue, 16 Jun 2020 07:46:02: 21000000 INFO @ Tue, 16 Jun 2020 07:46:05: 13000000 INFO @ Tue, 16 Jun 2020 07:46:06: 18000000 INFO @ Tue, 16 Jun 2020 07:46:09: 22000000 INFO @ Tue, 16 Jun 2020 07:46:12: 14000000 INFO @ Tue, 16 Jun 2020 07:46:12: 19000000 INFO @ Tue, 16 Jun 2020 07:46:16: 23000000 INFO @ Tue, 16 Jun 2020 07:46:18: 15000000 INFO @ Tue, 16 Jun 2020 07:46:18: 20000000 INFO @ Tue, 16 Jun 2020 07:46:23: 24000000 INFO @ Tue, 16 Jun 2020 07:46:25: 16000000 INFO @ Tue, 16 Jun 2020 07:46:25: 21000000 INFO @ Tue, 16 Jun 2020 07:46:29: 25000000 INFO @ Tue, 16 Jun 2020 07:46:31: 17000000 INFO @ Tue, 16 Jun 2020 07:46:31: 22000000 INFO @ Tue, 16 Jun 2020 07:46:36: 26000000 INFO @ Tue, 16 Jun 2020 07:46:38: 18000000 INFO @ Tue, 16 Jun 2020 07:46:38: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:46:43: 27000000 INFO @ Tue, 16 Jun 2020 07:46:44: 19000000 INFO @ Tue, 16 Jun 2020 07:46:44: 24000000 INFO @ Tue, 16 Jun 2020 07:46:45: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:46:45: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:46:45: #1 total tags in treatment: 27305766 INFO @ Tue, 16 Jun 2020 07:46:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:46:45: #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 07:46:46: #1 tags after filtering in treatment: 27305766 INFO @ Tue, 16 Jun 2020 07:46:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:46:46: #1 finished! INFO @ Tue, 16 Jun 2020 07:46:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:46:47: #2 number of paired peaks: 109 WARNING @ Tue, 16 Jun 2020 07:46:47: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 16 Jun 2020 07:46:47: start model_add_line... INFO @ Tue, 16 Jun 2020 07:46:48: start X-correlation... INFO @ Tue, 16 Jun 2020 07:46:48: end of X-cor INFO @ Tue, 16 Jun 2020 07:46:48: #2 finished! INFO @ Tue, 16 Jun 2020 07:46:48: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:46:48: #2 alternative fragment length(s) may be 1,32,142,527,545,547 bps INFO @ Tue, 16 Jun 2020 07:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.05_model.r WARNING @ Tue, 16 Jun 2020 07:46:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:46:48: #2 You may need to consider one of the other alternative d(s): 1,32,142,527,545,547 WARNING @ Tue, 16 Jun 2020 07:46:48: #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 07:46:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:46:50: 25000000 INFO @ Tue, 16 Jun 2020 07:46:50: 20000000 INFO @ Tue, 16 Jun 2020 07:46:56: 26000000 INFO @ Tue, 16 Jun 2020 07:46:56: 21000000 INFO @ Tue, 16 Jun 2020 07:47:02: 27000000 INFO @ Tue, 16 Jun 2020 07:47:02: 22000000 INFO @ Tue, 16 Jun 2020 07:47:04: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:47:04: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:47:04: #1 total tags in treatment: 27305766 INFO @ Tue, 16 Jun 2020 07:47:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:04: #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 07:47:04: #1 tags after filtering in treatment: 27305766 INFO @ Tue, 16 Jun 2020 07:47:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:04: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:06: #2 number of paired peaks: 109 WARNING @ Tue, 16 Jun 2020 07:47:06: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 16 Jun 2020 07:47:06: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:06: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:47:06: #2 alternative fragment length(s) may be 1,32,142,527,545,547 bps INFO @ Tue, 16 Jun 2020 07:47:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.10_model.r WARNING @ Tue, 16 Jun 2020 07:47:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:47:06: #2 You may need to consider one of the other alternative d(s): 1,32,142,527,545,547 WARNING @ Tue, 16 Jun 2020 07:47:06: #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 07:47:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:08: 23000000 INFO @ Tue, 16 Jun 2020 07:47:13: 24000000 INFO @ Tue, 16 Jun 2020 07:47:18: 25000000 INFO @ Tue, 16 Jun 2020 07:47:24: 26000000 INFO @ Tue, 16 Jun 2020 07:47:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:29: 27000000 INFO @ Tue, 16 Jun 2020 07:47:31: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:47:31: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:47:31: #1 total tags in treatment: 27305766 INFO @ Tue, 16 Jun 2020 07:47:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:31: #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 07:47:31: #1 tags after filtering in treatment: 27305766 INFO @ Tue, 16 Jun 2020 07:47:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:31: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:33: #2 number of paired peaks: 109 WARNING @ Tue, 16 Jun 2020 07:47:33: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 16 Jun 2020 07:47:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:33: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:47:33: #2 alternative fragment length(s) may be 1,32,142,527,545,547 bps INFO @ Tue, 16 Jun 2020 07:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.20_model.r WARNING @ Tue, 16 Jun 2020 07:47:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:47:33: #2 You may need to consider one of the other alternative d(s): 1,32,142,527,545,547 WARNING @ Tue, 16 Jun 2020 07:47:33: #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 07:47:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:47:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.05_summits.bed INFO @ Tue, 16 Jun 2020 07:47:47: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:48:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.10_summits.bed INFO @ Tue, 16 Jun 2020 07:48:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:48:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059266/SRX059266.20_summits.bed INFO @ Tue, 16 Jun 2020 07:48:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling