Job ID = 14159425 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: 00:05:54 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: 00:05:54 Overall time: 00:05:54 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 21:48:30: # 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 @ Wed, 08 Dec 2021 21:48:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:48:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:48:36: 1000000 INFO @ Wed, 08 Dec 2021 21:48:42: 2000000 INFO @ Wed, 08 Dec 2021 21:48:48: 3000000 INFO @ Wed, 08 Dec 2021 21:48:54: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 21:48:59: 5000000 INFO @ Wed, 08 Dec 2021 21:49:00: # 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 @ Wed, 08 Dec 2021 21:49:00: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:49:00: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:49:06: 6000000 INFO @ Wed, 08 Dec 2021 21:49:06: 1000000 INFO @ Wed, 08 Dec 2021 21:49:12: 2000000 INFO @ Wed, 08 Dec 2021 21:49:12: 7000000 INFO @ Wed, 08 Dec 2021 21:49:17: 3000000 INFO @ Wed, 08 Dec 2021 21:49:18: 8000000 INFO @ Wed, 08 Dec 2021 21:49:23: 4000000 INFO @ Wed, 08 Dec 2021 21:49:24: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 21:49:29: 5000000 INFO @ Wed, 08 Dec 2021 21:49:30: # 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 @ Wed, 08 Dec 2021 21:49:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:49:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:49:31: 10000000 INFO @ Wed, 08 Dec 2021 21:49:34: 6000000 INFO @ Wed, 08 Dec 2021 21:49:36: 1000000 INFO @ Wed, 08 Dec 2021 21:49:37: 11000000 INFO @ Wed, 08 Dec 2021 21:49:40: 7000000 INFO @ Wed, 08 Dec 2021 21:49:43: 2000000 INFO @ Wed, 08 Dec 2021 21:49:43: 12000000 INFO @ Wed, 08 Dec 2021 21:49:46: 8000000 INFO @ Wed, 08 Dec 2021 21:49:49: 3000000 INFO @ Wed, 08 Dec 2021 21:49:49: 13000000 INFO @ Wed, 08 Dec 2021 21:49:51: 9000000 INFO @ Wed, 08 Dec 2021 21:49:55: 4000000 INFO @ Wed, 08 Dec 2021 21:49:55: 14000000 INFO @ Wed, 08 Dec 2021 21:49:57: 10000000 INFO @ Wed, 08 Dec 2021 21:50:02: 15000000 INFO @ Wed, 08 Dec 2021 21:50:02: 5000000 INFO @ Wed, 08 Dec 2021 21:50:02: 11000000 INFO @ Wed, 08 Dec 2021 21:50:08: 6000000 INFO @ Wed, 08 Dec 2021 21:50:08: 16000000 INFO @ Wed, 08 Dec 2021 21:50:08: 12000000 INFO @ Wed, 08 Dec 2021 21:50:14: 13000000 INFO @ Wed, 08 Dec 2021 21:50:14: 7000000 INFO @ Wed, 08 Dec 2021 21:50:14: 17000000 INFO @ Wed, 08 Dec 2021 21:50:19: 14000000 INFO @ Wed, 08 Dec 2021 21:50:21: 8000000 INFO @ Wed, 08 Dec 2021 21:50:21: 18000000 INFO @ Wed, 08 Dec 2021 21:50:25: 15000000 INFO @ Wed, 08 Dec 2021 21:50:27: 9000000 INFO @ Wed, 08 Dec 2021 21:50:27: 19000000 INFO @ Wed, 08 Dec 2021 21:50:31: 16000000 INFO @ Wed, 08 Dec 2021 21:50:33: 10000000 INFO @ Wed, 08 Dec 2021 21:50:33: 20000000 INFO @ Wed, 08 Dec 2021 21:50:37: 17000000 INFO @ Wed, 08 Dec 2021 21:50:39: 11000000 INFO @ Wed, 08 Dec 2021 21:50:40: 21000000 INFO @ Wed, 08 Dec 2021 21:50:42: 18000000 INFO @ Wed, 08 Dec 2021 21:50:46: 12000000 INFO @ Wed, 08 Dec 2021 21:50:46: 22000000 INFO @ Wed, 08 Dec 2021 21:50:48: 19000000 INFO @ Wed, 08 Dec 2021 21:50:52: 13000000 INFO @ Wed, 08 Dec 2021 21:50:52: 23000000 INFO @ Wed, 08 Dec 2021 21:50:54: 20000000 INFO @ Wed, 08 Dec 2021 21:50:56: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:50:56: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:50:56: #1 total tags in treatment: 23558892 INFO @ Wed, 08 Dec 2021 21:50:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:50:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:50:56: #1 tags after filtering in treatment: 23558892 INFO @ Wed, 08 Dec 2021 21:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:50:56: #1 finished! INFO @ Wed, 08 Dec 2021 21:50:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:50:58: #2 number of paired peaks: 147 WARNING @ Wed, 08 Dec 2021 21:50:58: 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 @ Wed, 08 Dec 2021 21:50:58: start model_add_line... INFO @ Wed, 08 Dec 2021 21:50:58: start X-correlation... INFO @ Wed, 08 Dec 2021 21:50:58: end of X-cor INFO @ Wed, 08 Dec 2021 21:50:58: #2 finished! INFO @ Wed, 08 Dec 2021 21:50:58: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:50:58: #2 alternative fragment length(s) may be 1,12,15,23,46,121,522,553 bps INFO @ Wed, 08 Dec 2021 21:50:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.05_model.r WARNING @ Wed, 08 Dec 2021 21:50:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:50:58: #2 You may need to consider one of the other alternative d(s): 1,12,15,23,46,121,522,553 WARNING @ Wed, 08 Dec 2021 21:50:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:50:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:50:58: 14000000 INFO @ Wed, 08 Dec 2021 21:50:59: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:51:04: 15000000 INFO @ Wed, 08 Dec 2021 21:51:05: 22000000 INFO @ Wed, 08 Dec 2021 21:51:11: 16000000 INFO @ Wed, 08 Dec 2021 21:51:11: 23000000 INFO @ Wed, 08 Dec 2021 21:51:14: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:51:14: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:51:14: #1 total tags in treatment: 23558892 INFO @ Wed, 08 Dec 2021 21:51:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:51:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:51:14: #1 tags after filtering in treatment: 23558892 INFO @ Wed, 08 Dec 2021 21:51:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:51:14: #1 finished! INFO @ Wed, 08 Dec 2021 21:51:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:51:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:51:16: #2 number of paired peaks: 147 WARNING @ Wed, 08 Dec 2021 21:51:16: 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 @ Wed, 08 Dec 2021 21:51:16: start model_add_line... INFO @ Wed, 08 Dec 2021 21:51:16: start X-correlation... INFO @ Wed, 08 Dec 2021 21:51:16: end of X-cor INFO @ Wed, 08 Dec 2021 21:51:16: #2 finished! INFO @ Wed, 08 Dec 2021 21:51:16: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:51:16: #2 alternative fragment length(s) may be 1,12,15,23,46,121,522,553 bps INFO @ Wed, 08 Dec 2021 21:51:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.10_model.r WARNING @ Wed, 08 Dec 2021 21:51:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:51:16: #2 You may need to consider one of the other alternative d(s): 1,12,15,23,46,121,522,553 WARNING @ Wed, 08 Dec 2021 21:51:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:51:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:51:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:51:17: 17000000 INFO @ Wed, 08 Dec 2021 21:51:23: 18000000 INFO @ Wed, 08 Dec 2021 21:51:29: 19000000 INFO @ Wed, 08 Dec 2021 21:51:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:51:35: 20000000 INFO @ Wed, 08 Dec 2021 21:51:41: 21000000 INFO @ Wed, 08 Dec 2021 21:51:47: 22000000 INFO @ Wed, 08 Dec 2021 21:51:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:51:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:51:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.05_summits.bed INFO @ Wed, 08 Dec 2021 21:51:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:51:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:51:52: 23000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:51:56: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:51:56: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:51:56: #1 total tags in treatment: 23558892 INFO @ Wed, 08 Dec 2021 21:51:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:51:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:51:56: #1 tags after filtering in treatment: 23558892 INFO @ Wed, 08 Dec 2021 21:51:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:51:56: #1 finished! INFO @ Wed, 08 Dec 2021 21:51:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:51:58: #2 number of paired peaks: 147 WARNING @ Wed, 08 Dec 2021 21:51:58: 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 @ Wed, 08 Dec 2021 21:51:58: start model_add_line... INFO @ Wed, 08 Dec 2021 21:51:58: start X-correlation... INFO @ Wed, 08 Dec 2021 21:51:58: end of X-cor INFO @ Wed, 08 Dec 2021 21:51:58: #2 finished! INFO @ Wed, 08 Dec 2021 21:51:58: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:51:58: #2 alternative fragment length(s) may be 1,12,15,23,46,121,522,553 bps INFO @ Wed, 08 Dec 2021 21:51:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.20_model.r WARNING @ Wed, 08 Dec 2021 21:51:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:51:58: #2 You may need to consider one of the other alternative d(s): 1,12,15,23,46,121,522,553 WARNING @ Wed, 08 Dec 2021 21:51:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:51:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:51:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.10_summits.bed INFO @ Wed, 08 Dec 2021 21:52:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:52:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:52:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:52:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:52:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120616/SRX9120616.20_summits.bed INFO @ Wed, 08 Dec 2021 21:52:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling