Job ID = 6369025 SRX = SRX982090 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:34:25 prefetch.2.10.7: 1) Downloading 'SRR1956577'... 2020-06-16T00:34:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:16 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:16 prefetch.2.10.7: 1) 'SRR1956577' was downloaded successfully Read 18464702 spots for SRR1956577/SRR1956577.sra Written 18464702 spots for SRR1956577/SRR1956577.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: 00:04:07 18464702 reads; of these: 18464702 (100.00%) were unpaired; of these: 180689 (0.98%) aligned 0 times 15064173 (81.58%) aligned exactly 1 time 3219840 (17.44%) aligned >1 times 99.02% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 1792479 / 18284013 = 0.0980 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 09:47:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.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 09:47:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:29: 1000000 INFO @ Tue, 16 Jun 2020 09:47:37: 2000000 INFO @ Tue, 16 Jun 2020 09:47:44: 3000000 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 09:47:52: 4000000 INFO @ Tue, 16 Jun 2020 09:47:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.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 09:47:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:58: 1000000 INFO @ Tue, 16 Jun 2020 09:48:00: 5000000 INFO @ Tue, 16 Jun 2020 09:48:04: 2000000 INFO @ Tue, 16 Jun 2020 09:48:08: 6000000 INFO @ Tue, 16 Jun 2020 09:48:10: 3000000 INFO @ Tue, 16 Jun 2020 09:48:15: 7000000 INFO @ Tue, 16 Jun 2020 09:48:16: 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 @ Tue, 16 Jun 2020 09:48:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.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 09:48:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:22: 5000000 INFO @ Tue, 16 Jun 2020 09:48:22: 8000000 INFO @ Tue, 16 Jun 2020 09:48:29: 6000000 INFO @ Tue, 16 Jun 2020 09:48:29: 1000000 INFO @ Tue, 16 Jun 2020 09:48:30: 9000000 INFO @ Tue, 16 Jun 2020 09:48:35: 7000000 INFO @ Tue, 16 Jun 2020 09:48:35: 2000000 INFO @ Tue, 16 Jun 2020 09:48:38: 10000000 INFO @ Tue, 16 Jun 2020 09:48:42: 3000000 INFO @ Tue, 16 Jun 2020 09:48:42: 8000000 INFO @ Tue, 16 Jun 2020 09:48:46: 11000000 INFO @ Tue, 16 Jun 2020 09:48:48: 4000000 INFO @ Tue, 16 Jun 2020 09:48:48: 9000000 INFO @ Tue, 16 Jun 2020 09:48:53: 12000000 INFO @ Tue, 16 Jun 2020 09:48:55: 5000000 INFO @ Tue, 16 Jun 2020 09:48:55: 10000000 INFO @ Tue, 16 Jun 2020 09:49:01: 13000000 INFO @ Tue, 16 Jun 2020 09:49:01: 6000000 INFO @ Tue, 16 Jun 2020 09:49:01: 11000000 INFO @ Tue, 16 Jun 2020 09:49:08: 7000000 INFO @ Tue, 16 Jun 2020 09:49:08: 12000000 INFO @ Tue, 16 Jun 2020 09:49:08: 14000000 INFO @ Tue, 16 Jun 2020 09:49:14: 8000000 INFO @ Tue, 16 Jun 2020 09:49:14: 13000000 INFO @ Tue, 16 Jun 2020 09:49:15: 15000000 INFO @ Tue, 16 Jun 2020 09:49:21: 9000000 INFO @ Tue, 16 Jun 2020 09:49:21: 14000000 INFO @ Tue, 16 Jun 2020 09:49:21: 16000000 INFO @ Tue, 16 Jun 2020 09:49:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:24: #1 total tags in treatment: 16491534 INFO @ Tue, 16 Jun 2020 09:49:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:24: #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 09:49:25: #1 tags after filtering in treatment: 16491534 INFO @ Tue, 16 Jun 2020 09:49:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:26: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:49:26: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:26: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:49:26: #2 alternative fragment length(s) may be 2,28,581 bps INFO @ Tue, 16 Jun 2020 09:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.05_model.r WARNING @ Tue, 16 Jun 2020 09:49:26: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:26: #2 You may need to consider one of the other alternative d(s): 2,28,581 WARNING @ Tue, 16 Jun 2020 09:49:26: #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 09:49:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:27: 10000000 INFO @ Tue, 16 Jun 2020 09:49:28: 15000000 INFO @ Tue, 16 Jun 2020 09:49:34: 11000000 INFO @ Tue, 16 Jun 2020 09:49:34: 16000000 INFO @ Tue, 16 Jun 2020 09:49:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:37: #1 total tags in treatment: 16491534 INFO @ Tue, 16 Jun 2020 09:49:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:37: #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 09:49:37: #1 tags after filtering in treatment: 16491534 INFO @ Tue, 16 Jun 2020 09:49:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:38: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:49:38: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:39: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:49:39: #2 alternative fragment length(s) may be 2,28,581 bps INFO @ Tue, 16 Jun 2020 09:49:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.10_model.r WARNING @ Tue, 16 Jun 2020 09:49:39: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:39: #2 You may need to consider one of the other alternative d(s): 2,28,581 WARNING @ Tue, 16 Jun 2020 09:49:39: #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 09:49:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:40: 12000000 INFO @ Tue, 16 Jun 2020 09:49:45: 13000000 INFO @ Tue, 16 Jun 2020 09:49:51: 14000000 INFO @ Tue, 16 Jun 2020 09:49:51: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:49:57: 15000000 INFO @ Tue, 16 Jun 2020 09:50:02: 16000000 INFO @ Tue, 16 Jun 2020 09:50:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.05_summits.bed INFO @ Tue, 16 Jun 2020 09:50:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:05: #1 total tags in treatment: 16491534 INFO @ Tue, 16 Jun 2020 09:50:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:05: #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 09:50:06: #1 tags after filtering in treatment: 16491534 INFO @ Tue, 16 Jun 2020 09:50:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:07: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:50:07: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:07: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:50:07: #2 alternative fragment length(s) may be 2,28,581 bps INFO @ Tue, 16 Jun 2020 09:50:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.20_model.r WARNING @ Tue, 16 Jun 2020 09:50:07: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:07: #2 You may need to consider one of the other alternative d(s): 2,28,581 WARNING @ Tue, 16 Jun 2020 09:50:07: #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 09:50:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.10_summits.bed INFO @ Tue, 16 Jun 2020 09:50:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982090/SRX982090.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling