Job ID = 6507838 SRX = SRX494837 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:01:26 prefetch.2.10.7: 1) Downloading 'SRR1198369'... 2020-06-26T13:01:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:08:03 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:08:03 prefetch.2.10.7: 1) 'SRR1198369' was downloaded successfully 2020-06-26T13:08:03 prefetch.2.10.7: 'SRR1198369' has 0 unresolved dependencies Read 40075123 spots for SRR1198369/SRR1198369.sra Written 40075123 spots for SRR1198369/SRR1198369.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: 00:15:16 40075123 reads; of these: 40075123 (100.00%) were unpaired; of these: 1276018 (3.18%) aligned 0 times 32481526 (81.05%) aligned exactly 1 time 6317579 (15.76%) aligned >1 times 96.82% overall alignment rate Time searching: 00:15:16 Overall time: 00:15:16 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] 20130070 / 38799105 = 0.5188 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 @ Fri, 26 Jun 2020 22:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.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 @ Fri, 26 Jun 2020 22:43:04: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:43:04: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:43:10: 1000000 INFO @ Fri, 26 Jun 2020 22:43:15: 2000000 INFO @ Fri, 26 Jun 2020 22:43:22: 3000000 INFO @ Fri, 26 Jun 2020 22:43:28: 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 @ Fri, 26 Jun 2020 22:43:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.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 @ Fri, 26 Jun 2020 22:43:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:43:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:43:34: 5000000 INFO @ Fri, 26 Jun 2020 22:43:39: 1000000 INFO @ Fri, 26 Jun 2020 22:43:41: 6000000 INFO @ Fri, 26 Jun 2020 22:43:45: 2000000 INFO @ Fri, 26 Jun 2020 22:43:47: 7000000 INFO @ Fri, 26 Jun 2020 22:43:51: 3000000 INFO @ Fri, 26 Jun 2020 22:43:53: 8000000 INFO @ Fri, 26 Jun 2020 22:43:57: 4000000 INFO @ Fri, 26 Jun 2020 22:43:59: 9000000 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 @ Fri, 26 Jun 2020 22:44:03: 5000000 INFO @ Fri, 26 Jun 2020 22:44:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.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 @ Fri, 26 Jun 2020 22:44:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:44:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:44:08: 10000000 INFO @ Fri, 26 Jun 2020 22:44:10: 6000000 INFO @ Fri, 26 Jun 2020 22:44:12: 1000000 INFO @ Fri, 26 Jun 2020 22:44:13: 11000000 INFO @ Fri, 26 Jun 2020 22:44:18: 7000000 INFO @ Fri, 26 Jun 2020 22:44:20: 12000000 INFO @ Fri, 26 Jun 2020 22:44:20: 2000000 INFO @ Fri, 26 Jun 2020 22:44:25: 8000000 INFO @ Fri, 26 Jun 2020 22:44:26: 13000000 INFO @ Fri, 26 Jun 2020 22:44:26: 3000000 INFO @ Fri, 26 Jun 2020 22:44:32: 9000000 INFO @ Fri, 26 Jun 2020 22:44:33: 4000000 INFO @ Fri, 26 Jun 2020 22:44:33: 14000000 INFO @ Fri, 26 Jun 2020 22:44:40: 10000000 INFO @ Fri, 26 Jun 2020 22:44:41: 15000000 INFO @ Fri, 26 Jun 2020 22:44:43: 5000000 INFO @ Fri, 26 Jun 2020 22:44:47: 16000000 INFO @ Fri, 26 Jun 2020 22:44:47: 11000000 INFO @ Fri, 26 Jun 2020 22:44:51: 6000000 INFO @ Fri, 26 Jun 2020 22:44:54: 17000000 INFO @ Fri, 26 Jun 2020 22:44:55: 12000000 INFO @ Fri, 26 Jun 2020 22:44:58: 7000000 INFO @ Fri, 26 Jun 2020 22:45:00: 18000000 INFO @ Fri, 26 Jun 2020 22:45:02: 13000000 INFO @ Fri, 26 Jun 2020 22:45:04: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 22:45:04: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 22:45:04: #1 total tags in treatment: 18669035 INFO @ Fri, 26 Jun 2020 22:45:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:45:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:45:04: #1 tags after filtering in treatment: 18669035 INFO @ Fri, 26 Jun 2020 22:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:45:04: #1 finished! INFO @ Fri, 26 Jun 2020 22:45:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:45:06: 8000000 INFO @ Fri, 26 Jun 2020 22:45:06: #2 number of paired peaks: 287 WARNING @ Fri, 26 Jun 2020 22:45:06: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Fri, 26 Jun 2020 22:45:06: start model_add_line... INFO @ Fri, 26 Jun 2020 22:45:06: start X-correlation... INFO @ Fri, 26 Jun 2020 22:45:06: end of X-cor INFO @ Fri, 26 Jun 2020 22:45:06: #2 finished! INFO @ Fri, 26 Jun 2020 22:45:06: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:45:06: #2 alternative fragment length(s) may be 1,44,62,554 bps INFO @ Fri, 26 Jun 2020 22:45:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.05_model.r WARNING @ Fri, 26 Jun 2020 22:45:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:45:06: #2 You may need to consider one of the other alternative d(s): 1,44,62,554 WARNING @ Fri, 26 Jun 2020 22:45:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:45:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:45:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:45:10: 14000000 INFO @ Fri, 26 Jun 2020 22:45:13: 9000000 INFO @ Fri, 26 Jun 2020 22:45:16: 15000000 INFO @ Fri, 26 Jun 2020 22:45:21: 10000000 INFO @ Fri, 26 Jun 2020 22:45:23: 16000000 INFO @ Fri, 26 Jun 2020 22:45:29: 11000000 INFO @ Fri, 26 Jun 2020 22:45:31: 17000000 INFO @ Fri, 26 Jun 2020 22:45:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:45:37: 12000000 INFO @ Fri, 26 Jun 2020 22:45:38: 18000000 INFO @ Fri, 26 Jun 2020 22:45:43: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 22:45:43: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 22:45:43: #1 total tags in treatment: 18669035 INFO @ Fri, 26 Jun 2020 22:45:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:45:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:45:43: #1 tags after filtering in treatment: 18669035 INFO @ Fri, 26 Jun 2020 22:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:45:43: #1 finished! INFO @ Fri, 26 Jun 2020 22:45:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:45:43: 13000000 INFO @ Fri, 26 Jun 2020 22:45:44: #2 number of paired peaks: 287 WARNING @ Fri, 26 Jun 2020 22:45:44: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Fri, 26 Jun 2020 22:45:44: start model_add_line... INFO @ Fri, 26 Jun 2020 22:45:45: start X-correlation... INFO @ Fri, 26 Jun 2020 22:45:45: end of X-cor INFO @ Fri, 26 Jun 2020 22:45:45: #2 finished! INFO @ Fri, 26 Jun 2020 22:45:45: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:45:45: #2 alternative fragment length(s) may be 1,44,62,554 bps INFO @ Fri, 26 Jun 2020 22:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.10_model.r WARNING @ Fri, 26 Jun 2020 22:45:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:45:45: #2 You may need to consider one of the other alternative d(s): 1,44,62,554 WARNING @ Fri, 26 Jun 2020 22:45:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:45:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:45:50: 14000000 INFO @ Fri, 26 Jun 2020 22:45:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:45:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:45:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.05_summits.bed INFO @ Fri, 26 Jun 2020 22:45:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:45:56: 15000000 INFO @ Fri, 26 Jun 2020 22:46:02: 16000000 INFO @ Fri, 26 Jun 2020 22:46:08: 17000000 INFO @ Fri, 26 Jun 2020 22:46:15: 18000000 INFO @ Fri, 26 Jun 2020 22:46:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:46:19: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 22:46:19: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 22:46:19: #1 total tags in treatment: 18669035 INFO @ Fri, 26 Jun 2020 22:46:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:46:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:46:19: #1 tags after filtering in treatment: 18669035 INFO @ Fri, 26 Jun 2020 22:46:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:46:19: #1 finished! INFO @ Fri, 26 Jun 2020 22:46:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:46:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:46:21: #2 number of paired peaks: 287 WARNING @ Fri, 26 Jun 2020 22:46:21: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Fri, 26 Jun 2020 22:46:21: start model_add_line... INFO @ Fri, 26 Jun 2020 22:46:21: start X-correlation... INFO @ Fri, 26 Jun 2020 22:46:21: end of X-cor INFO @ Fri, 26 Jun 2020 22:46:21: #2 finished! INFO @ Fri, 26 Jun 2020 22:46:21: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:46:21: #2 alternative fragment length(s) may be 1,44,62,554 bps INFO @ Fri, 26 Jun 2020 22:46:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.20_model.r WARNING @ Fri, 26 Jun 2020 22:46:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:46:21: #2 You may need to consider one of the other alternative d(s): 1,44,62,554 WARNING @ Fri, 26 Jun 2020 22:46:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:46:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:46:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:46:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:46:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:46:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.10_summits.bed INFO @ Fri, 26 Jun 2020 22:46:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:46:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:47:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:47:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494837/SRX494837.20_summits.bed INFO @ Fri, 26 Jun 2020 22:47:03: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。