Job ID = 6507832 SRX = SRX494834 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:37:03 prefetch.2.10.7: 1) Downloading 'SRR1198366'... 2020-06-26T13:37:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:40:57 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:40:57 prefetch.2.10.7: 1) 'SRR1198366' was downloaded successfully Read 28363255 spots for SRR1198366/SRR1198366.sra Written 28363255 spots for SRR1198366/SRR1198366.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: 00:06:51 28363255 reads; of these: 28363255 (100.00%) were unpaired; of these: 608168 (2.14%) aligned 0 times 22697151 (80.02%) aligned exactly 1 time 5057936 (17.83%) aligned >1 times 97.86% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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 12 files... [bam_rmdupse_core] 8988989 / 27755087 = 0.3239 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 @ Fri, 26 Jun 2020 22:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.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 @ Fri, 26 Jun 2020 22:55:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:55:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:56:00: 1000000 INFO @ Fri, 26 Jun 2020 22:56:07: 2000000 INFO @ Fri, 26 Jun 2020 22:56:13: 3000000 INFO @ Fri, 26 Jun 2020 22:56:20: 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 @ Fri, 26 Jun 2020 22:56:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.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 @ Fri, 26 Jun 2020 22:56:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:56:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:56:26: 5000000 INFO @ Fri, 26 Jun 2020 22:56:31: 1000000 INFO @ Fri, 26 Jun 2020 22:56:33: 6000000 INFO @ Fri, 26 Jun 2020 22:56:38: 2000000 INFO @ Fri, 26 Jun 2020 22:56:40: 7000000 INFO @ Fri, 26 Jun 2020 22:56:45: 3000000 INFO @ Fri, 26 Jun 2020 22:56:47: 8000000 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 @ Fri, 26 Jun 2020 22:56:52: 4000000 INFO @ Fri, 26 Jun 2020 22:56:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.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 @ Fri, 26 Jun 2020 22:56:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:56:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:56:54: 9000000 INFO @ Fri, 26 Jun 2020 22:57:00: 5000000 INFO @ Fri, 26 Jun 2020 22:57:00: 1000000 INFO @ Fri, 26 Jun 2020 22:57:01: 10000000 INFO @ Fri, 26 Jun 2020 22:57:07: 6000000 INFO @ Fri, 26 Jun 2020 22:57:07: 2000000 INFO @ Fri, 26 Jun 2020 22:57:09: 11000000 INFO @ Fri, 26 Jun 2020 22:57:14: 7000000 INFO @ Fri, 26 Jun 2020 22:57:15: 3000000 INFO @ Fri, 26 Jun 2020 22:57:16: 12000000 INFO @ Fri, 26 Jun 2020 22:57:22: 4000000 INFO @ Fri, 26 Jun 2020 22:57:22: 8000000 INFO @ Fri, 26 Jun 2020 22:57:23: 13000000 INFO @ Fri, 26 Jun 2020 22:57:29: 5000000 INFO @ Fri, 26 Jun 2020 22:57:29: 9000000 INFO @ Fri, 26 Jun 2020 22:57:31: 14000000 INFO @ Fri, 26 Jun 2020 22:57:36: 6000000 INFO @ Fri, 26 Jun 2020 22:57:36: 10000000 INFO @ Fri, 26 Jun 2020 22:57:38: 15000000 INFO @ Fri, 26 Jun 2020 22:57:43: 7000000 INFO @ Fri, 26 Jun 2020 22:57:44: 11000000 INFO @ Fri, 26 Jun 2020 22:57:45: 16000000 INFO @ Fri, 26 Jun 2020 22:57:50: 8000000 INFO @ Fri, 26 Jun 2020 22:57:51: 12000000 INFO @ Fri, 26 Jun 2020 22:57:52: 17000000 INFO @ Fri, 26 Jun 2020 22:57:57: 9000000 INFO @ Fri, 26 Jun 2020 22:57:59: 13000000 INFO @ Fri, 26 Jun 2020 22:58:00: 18000000 INFO @ Fri, 26 Jun 2020 22:58:04: 10000000 INFO @ Fri, 26 Jun 2020 22:58:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:58:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:58:05: #1 total tags in treatment: 18766098 INFO @ Fri, 26 Jun 2020 22:58:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:58:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:58:06: #1 tags after filtering in treatment: 18766098 INFO @ Fri, 26 Jun 2020 22:58:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:58:06: #1 finished! INFO @ Fri, 26 Jun 2020 22:58:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:58:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:58:07: 14000000 INFO @ Fri, 26 Jun 2020 22:58:07: #2 number of paired peaks: 307 WARNING @ Fri, 26 Jun 2020 22:58:07: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 26 Jun 2020 22:58:07: start model_add_line... INFO @ Fri, 26 Jun 2020 22:58:07: start X-correlation... INFO @ Fri, 26 Jun 2020 22:58:07: end of X-cor INFO @ Fri, 26 Jun 2020 22:58:07: #2 finished! INFO @ Fri, 26 Jun 2020 22:58:07: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:58:07: #2 alternative fragment length(s) may be 1,29,43,542 bps INFO @ Fri, 26 Jun 2020 22:58:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.05_model.r WARNING @ Fri, 26 Jun 2020 22:58:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:58:07: #2 You may need to consider one of the other alternative d(s): 1,29,43,542 WARNING @ Fri, 26 Jun 2020 22:58:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:58:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:58:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:58:11: 11000000 INFO @ Fri, 26 Jun 2020 22:58:14: 15000000 INFO @ Fri, 26 Jun 2020 22:58:18: 12000000 INFO @ Fri, 26 Jun 2020 22:58:22: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:58:25: 13000000 INFO @ Fri, 26 Jun 2020 22:58:29: 17000000 INFO @ Fri, 26 Jun 2020 22:58:33: 14000000 INFO @ Fri, 26 Jun 2020 22:58:36: 18000000 INFO @ Fri, 26 Jun 2020 22:58:40: 15000000 INFO @ Fri, 26 Jun 2020 22:58:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:58:42: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:58:42: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:58:42: #1 total tags in treatment: 18766098 INFO @ Fri, 26 Jun 2020 22:58:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:58:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:58:42: #1 tags after filtering in treatment: 18766098 INFO @ Fri, 26 Jun 2020 22:58:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:58:42: #1 finished! INFO @ Fri, 26 Jun 2020 22:58:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:58:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:58:44: #2 number of paired peaks: 307 WARNING @ Fri, 26 Jun 2020 22:58:44: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 26 Jun 2020 22:58:44: start model_add_line... INFO @ Fri, 26 Jun 2020 22:58:44: start X-correlation... INFO @ Fri, 26 Jun 2020 22:58:44: end of X-cor INFO @ Fri, 26 Jun 2020 22:58:44: #2 finished! INFO @ Fri, 26 Jun 2020 22:58:44: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:58:44: #2 alternative fragment length(s) may be 1,29,43,542 bps INFO @ Fri, 26 Jun 2020 22:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.10_model.r WARNING @ Fri, 26 Jun 2020 22:58:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:58:44: #2 You may need to consider one of the other alternative d(s): 1,29,43,542 WARNING @ Fri, 26 Jun 2020 22:58:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:58:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:58:47: 16000000 INFO @ Fri, 26 Jun 2020 22:58:54: 17000000 INFO @ Fri, 26 Jun 2020 22:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.05_summits.bed INFO @ Fri, 26 Jun 2020 22:58:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:59:01: 18000000 INFO @ Fri, 26 Jun 2020 22:59:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:59:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:59:06: #1 total tags in treatment: 18766098 INFO @ Fri, 26 Jun 2020 22:59:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:59:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:59:06: #1 tags after filtering in treatment: 18766098 INFO @ Fri, 26 Jun 2020 22:59:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:59:06: #1 finished! INFO @ Fri, 26 Jun 2020 22:59:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:59:07: #2 number of paired peaks: 307 WARNING @ Fri, 26 Jun 2020 22:59:07: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 26 Jun 2020 22:59:07: start model_add_line... INFO @ Fri, 26 Jun 2020 22:59:08: start X-correlation... INFO @ Fri, 26 Jun 2020 22:59:08: end of X-cor INFO @ Fri, 26 Jun 2020 22:59:08: #2 finished! INFO @ Fri, 26 Jun 2020 22:59:08: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:59:08: #2 alternative fragment length(s) may be 1,29,43,542 bps INFO @ Fri, 26 Jun 2020 22:59:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.20_model.r WARNING @ Fri, 26 Jun 2020 22:59:08: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:59:08: #2 You may need to consider one of the other alternative d(s): 1,29,43,542 WARNING @ Fri, 26 Jun 2020 22:59:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:59:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:59:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:59:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.10_summits.bed INFO @ Fri, 26 Jun 2020 22:59:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:59:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:59:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:59:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:59:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494834/SRX494834.20_summits.bed INFO @ Fri, 26 Jun 2020 22:59:57: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling