Job ID = 10166094 SRX = SRX9120616 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: 00:06:09 28295530 reads; of these: 28295530 (100.00%) were unpaired; of these: 89064 (0.31%) aligned 0 times 23608907 (83.44%) aligned exactly 1 time 4597559 (16.25%) aligned >1 times 99.69% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:09 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] 4647574 / 28206466 = 0.1648 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 20:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.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 20:40:56: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:40:56: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:01: 1000000 INFO @ Thu, 08 Oct 2020 20:41:06: 2000000 INFO @ Thu, 08 Oct 2020 20:41:11: 3000000 INFO @ Thu, 08 Oct 2020 20:41:15: 4000000 INFO @ Thu, 08 Oct 2020 20:41:20: 5000000 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 20:41:25: 6000000 INFO @ Thu, 08 Oct 2020 20:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.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 20:41:26: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:26: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:31: 7000000 INFO @ Thu, 08 Oct 2020 20:41:32: 1000000 INFO @ Thu, 08 Oct 2020 20:41:36: 8000000 INFO @ Thu, 08 Oct 2020 20:41:38: 2000000 INFO @ Thu, 08 Oct 2020 20:41:42: 9000000 INFO @ Thu, 08 Oct 2020 20:41:44: 3000000 INFO @ Thu, 08 Oct 2020 20:41:47: 10000000 INFO @ Thu, 08 Oct 2020 20:41:50: 4000000 INFO @ Thu, 08 Oct 2020 20:41:52: 11000000 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 20:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.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 20:41:56: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:56: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:56: 5000000 INFO @ Thu, 08 Oct 2020 20:41:58: 12000000 INFO @ Thu, 08 Oct 2020 20:42:02: 1000000 INFO @ Thu, 08 Oct 2020 20:42:03: 6000000 INFO @ Thu, 08 Oct 2020 20:42:03: 13000000 INFO @ Thu, 08 Oct 2020 20:42:07: 2000000 INFO @ Thu, 08 Oct 2020 20:42:09: 7000000 INFO @ Thu, 08 Oct 2020 20:42:09: 14000000 INFO @ Thu, 08 Oct 2020 20:42:13: 3000000 INFO @ Thu, 08 Oct 2020 20:42:15: 15000000 INFO @ Thu, 08 Oct 2020 20:42:15: 8000000 INFO @ Thu, 08 Oct 2020 20:42:19: 4000000 INFO @ Thu, 08 Oct 2020 20:42:20: 16000000 INFO @ Thu, 08 Oct 2020 20:42:21: 9000000 INFO @ Thu, 08 Oct 2020 20:42:25: 5000000 INFO @ Thu, 08 Oct 2020 20:42:26: 17000000 INFO @ Thu, 08 Oct 2020 20:42:28: 10000000 INFO @ Thu, 08 Oct 2020 20:42:30: 6000000 INFO @ Thu, 08 Oct 2020 20:42:32: 18000000 INFO @ Thu, 08 Oct 2020 20:42:34: 11000000 INFO @ Thu, 08 Oct 2020 20:42:36: 7000000 INFO @ Thu, 08 Oct 2020 20:42:37: 19000000 INFO @ Thu, 08 Oct 2020 20:42:40: 12000000 INFO @ Thu, 08 Oct 2020 20:42:42: 8000000 INFO @ Thu, 08 Oct 2020 20:42:43: 20000000 INFO @ Thu, 08 Oct 2020 20:42:46: 13000000 INFO @ Thu, 08 Oct 2020 20:42:47: 9000000 INFO @ Thu, 08 Oct 2020 20:42:49: 21000000 INFO @ Thu, 08 Oct 2020 20:42:52: 14000000 INFO @ Thu, 08 Oct 2020 20:42:53: 10000000 INFO @ Thu, 08 Oct 2020 20:42:54: 22000000 INFO @ Thu, 08 Oct 2020 20:42:58: 15000000 INFO @ Thu, 08 Oct 2020 20:42:59: 11000000 INFO @ Thu, 08 Oct 2020 20:43:00: 23000000 INFO @ Thu, 08 Oct 2020 20:43:03: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:43:03: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:43:03: #1 total tags in treatment: 23558892 INFO @ Thu, 08 Oct 2020 20:43:03: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:03: #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 20:43:04: #1 tags after filtering in treatment: 23558892 INFO @ Thu, 08 Oct 2020 20:43:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:04: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:04: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:43:04: 12000000 INFO @ Thu, 08 Oct 2020 20:43:05: 16000000 INFO @ Thu, 08 Oct 2020 20:43:05: #2 number of paired peaks: 147 WARNING @ Thu, 08 Oct 2020 20:43:05: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Thu, 08 Oct 2020 20:43:05: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:05: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:05: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:05: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:05: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:43:05: #2 alternative fragment length(s) may be 1,12,15,23,46,121,522,553 bps INFO @ Thu, 08 Oct 2020 20:43:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.05_model.r WARNING @ Thu, 08 Oct 2020 20:43:05: #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 20:43:05: #2 You may need to consider one of the other alternative d(s): 1,12,15,23,46,121,522,553 WARNING @ Thu, 08 Oct 2020 20:43:05: #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 20:43:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:10: 13000000 INFO @ Thu, 08 Oct 2020 20:43:11: 17000000 INFO @ Thu, 08 Oct 2020 20:43:15: 14000000 INFO @ Thu, 08 Oct 2020 20:43:17: 18000000 INFO @ Thu, 08 Oct 2020 20:43:21: 15000000 INFO @ Thu, 08 Oct 2020 20:43:23: 19000000 INFO @ Thu, 08 Oct 2020 20:43:26: 16000000 INFO @ Thu, 08 Oct 2020 20:43:29: 20000000 INFO @ Thu, 08 Oct 2020 20:43:32: 17000000 INFO @ Thu, 08 Oct 2020 20:43:35: 21000000 INFO @ Thu, 08 Oct 2020 20:43:37: 18000000 INFO @ Thu, 08 Oct 2020 20:43:41: 22000000 INFO @ Thu, 08 Oct 2020 20:43:41: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:43:43: 19000000 INFO @ Thu, 08 Oct 2020 20:43:47: 23000000 INFO @ Thu, 08 Oct 2020 20:43:48: 20000000 INFO @ Thu, 08 Oct 2020 20:43:50: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:43:50: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:43:50: #1 total tags in treatment: 23558892 INFO @ Thu, 08 Oct 2020 20:43:50: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:50: #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 20:43:51: #1 tags after filtering in treatment: 23558892 INFO @ Thu, 08 Oct 2020 20:43:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:51: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:51: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:51: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:43:52: #2 number of paired peaks: 147 WARNING @ Thu, 08 Oct 2020 20:43:52: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Thu, 08 Oct 2020 20:43:52: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:52: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:52: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:52: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:52: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:43:52: #2 alternative fragment length(s) may be 1,12,15,23,46,121,522,553 bps INFO @ Thu, 08 Oct 2020 20:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.10_model.r WARNING @ Thu, 08 Oct 2020 20:43:52: #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 20:43:52: #2 You may need to consider one of the other alternative d(s): 1,12,15,23,46,121,522,553 WARNING @ Thu, 08 Oct 2020 20:43:52: #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 20:43:52: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:54: 21000000 INFO @ Thu, 08 Oct 2020 20:43:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:43:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:43:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.05_summits.bed INFO @ Thu, 08 Oct 2020 20:43:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:43:59: 22000000 INFO @ Thu, 08 Oct 2020 20:44:04: 23000000 INFO @ Thu, 08 Oct 2020 20:44:07: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:44:07: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:44:07: #1 total tags in treatment: 23558892 INFO @ Thu, 08 Oct 2020 20:44:07: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:44:07: #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 20:44:07: #1 tags after filtering in treatment: 23558892 INFO @ Thu, 08 Oct 2020 20:44:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:44:07: #1 finished! INFO @ Thu, 08 Oct 2020 20:44:07: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:44:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:44:08: #2 number of paired peaks: 147 WARNING @ Thu, 08 Oct 2020 20:44:08: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Thu, 08 Oct 2020 20:44:08: start model_add_line... INFO @ Thu, 08 Oct 2020 20:44:09: start X-correlation... INFO @ Thu, 08 Oct 2020 20:44:09: end of X-cor INFO @ Thu, 08 Oct 2020 20:44:09: #2 finished! INFO @ Thu, 08 Oct 2020 20:44:09: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:44:09: #2 alternative fragment length(s) may be 1,12,15,23,46,121,522,553 bps INFO @ Thu, 08 Oct 2020 20:44:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.20_model.r WARNING @ Thu, 08 Oct 2020 20:44:09: #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 20:44:09: #2 You may need to consider one of the other alternative d(s): 1,12,15,23,46,121,522,553 WARNING @ Thu, 08 Oct 2020 20:44:09: #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 20:44:09: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:44:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:44:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:44:44: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:44:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:44:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:44:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.10_summits.bed INFO @ Thu, 08 Oct 2020 20:44:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.20_summits.bed INFO @ Thu, 08 Oct 2020 20:45:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling