Job ID = 6368165 SRX = SRX494849 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:30 prefetch.2.10.7: 1) Downloading 'SRR1198381'... 2020-06-16T00:04:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:09:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:09:47 prefetch.2.10.7: 1) 'SRR1198381' was downloaded successfully Read 21509609 spots for SRR1198381/SRR1198381.sra Written 21509609 spots for SRR1198381/SRR1198381.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: 00:03:54 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255390 (1.19%) aligned 0 times 17821460 (82.85%) aligned exactly 1 time 3432759 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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 8 files... [bam_rmdupse_core] 3667519 / 21254219 = 0.1726 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 09:19:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.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 09:19:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:49: 1000000 INFO @ Tue, 16 Jun 2020 09:19:54: 2000000 INFO @ Tue, 16 Jun 2020 09:19:59: 3000000 INFO @ Tue, 16 Jun 2020 09:20:03: 4000000 INFO @ Tue, 16 Jun 2020 09:20:08: 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 @ Tue, 16 Jun 2020 09:20:13: 6000000 INFO @ Tue, 16 Jun 2020 09:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.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 09:20:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:17: 7000000 INFO @ Tue, 16 Jun 2020 09:20:19: 1000000 INFO @ Tue, 16 Jun 2020 09:20:22: 8000000 INFO @ Tue, 16 Jun 2020 09:20:24: 2000000 INFO @ Tue, 16 Jun 2020 09:20:27: 9000000 INFO @ Tue, 16 Jun 2020 09:20:29: 3000000 INFO @ Tue, 16 Jun 2020 09:20:32: 10000000 INFO @ Tue, 16 Jun 2020 09:20:34: 4000000 INFO @ Tue, 16 Jun 2020 09:20:37: 11000000 INFO @ Tue, 16 Jun 2020 09:20:39: 5000000 INFO @ Tue, 16 Jun 2020 09:20:41: 12000000 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 09:20:43: 6000000 INFO @ Tue, 16 Jun 2020 09:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.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 09:20:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:46: 13000000 INFO @ Tue, 16 Jun 2020 09:20:48: 7000000 INFO @ Tue, 16 Jun 2020 09:20:49: 1000000 INFO @ Tue, 16 Jun 2020 09:20:51: 14000000 INFO @ Tue, 16 Jun 2020 09:20:53: 8000000 INFO @ Tue, 16 Jun 2020 09:20:54: 2000000 INFO @ Tue, 16 Jun 2020 09:20:56: 15000000 INFO @ Tue, 16 Jun 2020 09:20:57: 9000000 INFO @ Tue, 16 Jun 2020 09:20:59: 3000000 INFO @ Tue, 16 Jun 2020 09:21:01: 16000000 INFO @ Tue, 16 Jun 2020 09:21:02: 10000000 INFO @ Tue, 16 Jun 2020 09:21:04: 4000000 INFO @ Tue, 16 Jun 2020 09:21:06: 17000000 INFO @ Tue, 16 Jun 2020 09:21:07: 11000000 INFO @ Tue, 16 Jun 2020 09:21:09: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:21:09: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:21:09: #1 total tags in treatment: 17586700 INFO @ Tue, 16 Jun 2020 09:21:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:09: #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 09:21:09: #1 tags after filtering in treatment: 17586700 INFO @ Tue, 16 Jun 2020 09:21:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:09: 5000000 INFO @ Tue, 16 Jun 2020 09:21:10: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 09:21:10: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:10: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:21:10: #2 alternative fragment length(s) may be 1,33,558 bps INFO @ Tue, 16 Jun 2020 09:21:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.05_model.r WARNING @ Tue, 16 Jun 2020 09:21:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:10: #2 You may need to consider one of the other alternative d(s): 1,33,558 WARNING @ Tue, 16 Jun 2020 09:21:10: #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 09:21:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:12: 12000000 INFO @ Tue, 16 Jun 2020 09:21:14: 6000000 INFO @ Tue, 16 Jun 2020 09:21:16: 13000000 INFO @ Tue, 16 Jun 2020 09:21:19: 7000000 INFO @ Tue, 16 Jun 2020 09:21:21: 14000000 INFO @ Tue, 16 Jun 2020 09:21:24: 8000000 INFO @ Tue, 16 Jun 2020 09:21:26: 15000000 INFO @ Tue, 16 Jun 2020 09:21:29: 9000000 INFO @ Tue, 16 Jun 2020 09:21:31: 16000000 INFO @ Tue, 16 Jun 2020 09:21:33: 10000000 INFO @ Tue, 16 Jun 2020 09:21:35: 17000000 INFO @ Tue, 16 Jun 2020 09:21:38: 11000000 INFO @ Tue, 16 Jun 2020 09:21:38: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:21:38: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:21:38: #1 total tags in treatment: 17586700 INFO @ Tue, 16 Jun 2020 09:21:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:38: #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 09:21:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:38: #1 tags after filtering in treatment: 17586700 INFO @ Tue, 16 Jun 2020 09:21:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:40: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 09:21:40: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:40: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:21:40: #2 alternative fragment length(s) may be 1,33,558 bps INFO @ Tue, 16 Jun 2020 09:21:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.10_model.r WARNING @ Tue, 16 Jun 2020 09:21:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:40: #2 You may need to consider one of the other alternative d(s): 1,33,558 WARNING @ Tue, 16 Jun 2020 09:21:40: #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 09:21:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:43: 12000000 INFO @ Tue, 16 Jun 2020 09:21:47: 13000000 INFO @ Tue, 16 Jun 2020 09:21:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.05_summits.bed INFO @ Tue, 16 Jun 2020 09:21:52: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:52: 14000000 INFO @ Tue, 16 Jun 2020 09:21:57: 15000000 INFO @ Tue, 16 Jun 2020 09:22:01: 16000000 INFO @ Tue, 16 Jun 2020 09:22:06: 17000000 INFO @ Tue, 16 Jun 2020 09:22:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:09: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:22:09: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:22:09: #1 total tags in treatment: 17586700 INFO @ Tue, 16 Jun 2020 09:22:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:09: #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 09:22:09: #1 tags after filtering in treatment: 17586700 INFO @ Tue, 16 Jun 2020 09:22:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:10: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 09:22:10: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:11: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:22:11: #2 alternative fragment length(s) may be 1,33,558 bps INFO @ Tue, 16 Jun 2020 09:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.20_model.r WARNING @ Tue, 16 Jun 2020 09:22:11: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:11: #2 You may need to consider one of the other alternative d(s): 1,33,558 WARNING @ Tue, 16 Jun 2020 09:22:11: #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 09:22:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:11: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:22:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.10_summits.bed INFO @ Tue, 16 Jun 2020 09:22:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494849/SRX494849.20_summits.bed INFO @ Tue, 16 Jun 2020 09:22:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。