Job ID = 10166090 SRX = SRX9120607 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:07:31 41837722 reads; of these: 41837722 (100.00%) were unpaired; of these: 11196918 (26.76%) aligned 0 times 25172664 (60.17%) aligned exactly 1 time 5468140 (13.07%) aligned >1 times 73.24% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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] 5983297 / 30640804 = 0.1953 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, 08 Oct 2020 20:42:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.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, 08 Oct 2020 20:42:56: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:56: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:43:01: 1000000 INFO @ Thu, 08 Oct 2020 20:43:06: 2000000 INFO @ Thu, 08 Oct 2020 20:43:11: 3000000 INFO @ Thu, 08 Oct 2020 20:43:15: 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 @ Thu, 08 Oct 2020 20:43:20: 5000000 INFO @ Thu, 08 Oct 2020 20:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.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, 08 Oct 2020 20:43:25: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:43:25: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:43:25: 6000000 INFO @ Thu, 08 Oct 2020 20:43:30: 7000000 INFO @ Thu, 08 Oct 2020 20:43:30: 1000000 INFO @ Thu, 08 Oct 2020 20:43:35: 8000000 INFO @ Thu, 08 Oct 2020 20:43:36: 2000000 INFO @ Thu, 08 Oct 2020 20:43:41: 9000000 INFO @ Thu, 08 Oct 2020 20:43:41: 3000000 INFO @ Thu, 08 Oct 2020 20:43:46: 10000000 INFO @ Thu, 08 Oct 2020 20:43:46: 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 @ Thu, 08 Oct 2020 20:43:51: 11000000 INFO @ Thu, 08 Oct 2020 20:43:51: 5000000 INFO @ Thu, 08 Oct 2020 20:43:56: 12000000 INFO @ Thu, 08 Oct 2020 20:43:56: 6000000 INFO @ Thu, 08 Oct 2020 20:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.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, 08 Oct 2020 20:43:57: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:43:57: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:44:01: 13000000 INFO @ Thu, 08 Oct 2020 20:44:02: 7000000 INFO @ Thu, 08 Oct 2020 20:44:02: 1000000 INFO @ Thu, 08 Oct 2020 20:44:07: 14000000 INFO @ Thu, 08 Oct 2020 20:44:07: 8000000 INFO @ Thu, 08 Oct 2020 20:44:07: 2000000 INFO @ Thu, 08 Oct 2020 20:44:12: 15000000 INFO @ Thu, 08 Oct 2020 20:44:12: 9000000 INFO @ Thu, 08 Oct 2020 20:44:13: 3000000 INFO @ Thu, 08 Oct 2020 20:44:17: 16000000 INFO @ Thu, 08 Oct 2020 20:44:17: 10000000 INFO @ Thu, 08 Oct 2020 20:44:18: 4000000 INFO @ Thu, 08 Oct 2020 20:44:22: 17000000 INFO @ Thu, 08 Oct 2020 20:44:23: 11000000 INFO @ Thu, 08 Oct 2020 20:44:23: 5000000 INFO @ Thu, 08 Oct 2020 20:44:27: 18000000 INFO @ Thu, 08 Oct 2020 20:44:28: 12000000 INFO @ Thu, 08 Oct 2020 20:44:28: 6000000 INFO @ Thu, 08 Oct 2020 20:44:33: 19000000 INFO @ Thu, 08 Oct 2020 20:44:33: 13000000 INFO @ Thu, 08 Oct 2020 20:44:34: 7000000 INFO @ Thu, 08 Oct 2020 20:44:38: 20000000 INFO @ Thu, 08 Oct 2020 20:44:38: 14000000 INFO @ Thu, 08 Oct 2020 20:44:39: 8000000 INFO @ Thu, 08 Oct 2020 20:44:43: 21000000 INFO @ Thu, 08 Oct 2020 20:44:44: 15000000 INFO @ Thu, 08 Oct 2020 20:44:44: 9000000 INFO @ Thu, 08 Oct 2020 20:44:49: 22000000 INFO @ Thu, 08 Oct 2020 20:44:49: 16000000 INFO @ Thu, 08 Oct 2020 20:44:50: 10000000 INFO @ Thu, 08 Oct 2020 20:44:54: 23000000 INFO @ Thu, 08 Oct 2020 20:44:54: 17000000 INFO @ Thu, 08 Oct 2020 20:44:55: 11000000 INFO @ Thu, 08 Oct 2020 20:44:59: 24000000 INFO @ Thu, 08 Oct 2020 20:45:00: 18000000 INFO @ Thu, 08 Oct 2020 20:45:00: 12000000 INFO @ Thu, 08 Oct 2020 20:45:03: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:45:03: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:45:03: #1 total tags in treatment: 24657507 INFO @ Thu, 08 Oct 2020 20:45:03: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:45:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:45:03: #1 tags after filtering in treatment: 24657507 INFO @ Thu, 08 Oct 2020 20:45:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:45:03: #1 finished! INFO @ Thu, 08 Oct 2020 20:45:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:45:04: #2 number of paired peaks: 173 WARNING @ Thu, 08 Oct 2020 20:45:04: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Thu, 08 Oct 2020 20:45:04: start model_add_line... INFO @ Thu, 08 Oct 2020 20:45:05: start X-correlation... INFO @ Thu, 08 Oct 2020 20:45:05: end of X-cor INFO @ Thu, 08 Oct 2020 20:45:05: #2 finished! INFO @ Thu, 08 Oct 2020 20:45:05: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:45:05: #2 alternative fragment length(s) may be 1,49,550,596 bps INFO @ Thu, 08 Oct 2020 20:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05_model.r WARNING @ Thu, 08 Oct 2020 20:45:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:45:05: #2 You may need to consider one of the other alternative d(s): 1,49,550,596 WARNING @ Thu, 08 Oct 2020 20:45:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:45:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:45:05: 19000000 INFO @ Thu, 08 Oct 2020 20:45:06: 13000000 INFO @ Thu, 08 Oct 2020 20:45:10: 20000000 INFO @ Thu, 08 Oct 2020 20:45:11: 14000000 INFO @ Thu, 08 Oct 2020 20:45:16: 21000000 INFO @ Thu, 08 Oct 2020 20:45:16: 15000000 INFO @ Thu, 08 Oct 2020 20:45:21: 22000000 INFO @ Thu, 08 Oct 2020 20:45:21: 16000000 INFO @ Thu, 08 Oct 2020 20:45:27: 23000000 INFO @ Thu, 08 Oct 2020 20:45:27: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:45:32: 24000000 INFO @ Thu, 08 Oct 2020 20:45:32: 18000000 INFO @ Thu, 08 Oct 2020 20:45:35: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:45:35: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:45:35: #1 total tags in treatment: 24657507 INFO @ Thu, 08 Oct 2020 20:45:35: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:45:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:45:35: #1 tags after filtering in treatment: 24657507 INFO @ Thu, 08 Oct 2020 20:45:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:45:35: #1 finished! INFO @ Thu, 08 Oct 2020 20:45:35: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:45:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:45:37: #2 number of paired peaks: 173 WARNING @ Thu, 08 Oct 2020 20:45:37: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Thu, 08 Oct 2020 20:45:37: start model_add_line... INFO @ Thu, 08 Oct 2020 20:45:37: 19000000 INFO @ Thu, 08 Oct 2020 20:45:37: start X-correlation... INFO @ Thu, 08 Oct 2020 20:45:37: end of X-cor INFO @ Thu, 08 Oct 2020 20:45:37: #2 finished! INFO @ Thu, 08 Oct 2020 20:45:37: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:45:37: #2 alternative fragment length(s) may be 1,49,550,596 bps INFO @ Thu, 08 Oct 2020 20:45:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10_model.r WARNING @ Thu, 08 Oct 2020 20:45:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:45:37: #2 You may need to consider one of the other alternative d(s): 1,49,550,596 WARNING @ Thu, 08 Oct 2020 20:45:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:45:37: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:45:42: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:45:42: 20000000 INFO @ Thu, 08 Oct 2020 20:45:47: 21000000 INFO @ Thu, 08 Oct 2020 20:45:52: 22000000 INFO @ Thu, 08 Oct 2020 20:45:57: 23000000 INFO @ Thu, 08 Oct 2020 20:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05_summits.bed INFO @ Thu, 08 Oct 2020 20:45:59: Done! INFO @ Thu, 08 Oct 2020 20:46:02: 24000000 INFO @ Thu, 08 Oct 2020 20:46:05: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:46:05: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:46:05: #1 total tags in treatment: 24657507 INFO @ Thu, 08 Oct 2020 20:46:05: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:46:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:46:05: #1 tags after filtering in treatment: 24657507 INFO @ Thu, 08 Oct 2020 20:46:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:46:05: #1 finished! INFO @ Thu, 08 Oct 2020 20:46:05: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:46:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:46:07: #2 number of paired peaks: 173 WARNING @ Thu, 08 Oct 2020 20:46:07: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Thu, 08 Oct 2020 20:46:07: start model_add_line... INFO @ Thu, 08 Oct 2020 20:46:07: start X-correlation... INFO @ Thu, 08 Oct 2020 20:46:07: end of X-cor INFO @ Thu, 08 Oct 2020 20:46:07: #2 finished! INFO @ Thu, 08 Oct 2020 20:46:07: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:46:07: #2 alternative fragment length(s) may be 1,49,550,596 bps INFO @ Thu, 08 Oct 2020 20:46:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20_model.r WARNING @ Thu, 08 Oct 2020 20:46:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:46:07: #2 You may need to consider one of the other alternative d(s): 1,49,550,596 WARNING @ Thu, 08 Oct 2020 20:46:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:46:07: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:46:07: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:46:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10_summits.bed INFO @ Thu, 08 Oct 2020 20:46:32: Done! INFO @ Thu, 08 Oct 2020 20:46:44: #3 Call peaks for each chromosome... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:47:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:47:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:47:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20_summits.bed INFO @ Thu, 08 Oct 2020 20:47:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling