Job ID = 6367693 SRX = SRX3942556 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:35 prefetch.2.10.7: 1) Downloading 'SRR7010077'... 2020-06-15T23:31:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:27 prefetch.2.10.7: 'SRR7010077' is valid 2020-06-15T23:33:27 prefetch.2.10.7: 1) 'SRR7010077' was downloaded successfully 2020-06-15T23:33:27 prefetch.2.10.7: 'SRR7010077' has 0 unresolved dependencies Read 14716059 spots for SRR7010077/SRR7010077.sra Written 14716059 spots for SRR7010077/SRR7010077.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: 00:05:22 14716059 reads; of these: 14716059 (100.00%) were unpaired; of these: 1292986 (8.79%) aligned 0 times 10731369 (72.92%) aligned exactly 1 time 2691704 (18.29%) aligned >1 times 91.21% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 2906050 / 13423073 = 0.2165 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 08:43:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.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 08:43:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:25: 1000000 INFO @ Tue, 16 Jun 2020 08:43:30: 2000000 INFO @ Tue, 16 Jun 2020 08:43:35: 3000000 INFO @ Tue, 16 Jun 2020 08:43:40: 4000000 INFO @ Tue, 16 Jun 2020 08:43:45: 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 08:43:50: 6000000 INFO @ Tue, 16 Jun 2020 08:43:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.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 08:43:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:55: 7000000 INFO @ Tue, 16 Jun 2020 08:43:56: 1000000 INFO @ Tue, 16 Jun 2020 08:44:00: 8000000 INFO @ Tue, 16 Jun 2020 08:44:02: 2000000 INFO @ Tue, 16 Jun 2020 08:44:05: 9000000 INFO @ Tue, 16 Jun 2020 08:44:08: 3000000 INFO @ Tue, 16 Jun 2020 08:44:10: 10000000 INFO @ Tue, 16 Jun 2020 08:44:13: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:44:13: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:44:13: #1 total tags in treatment: 10517023 INFO @ Tue, 16 Jun 2020 08:44:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:13: #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 08:44:13: #1 tags after filtering in treatment: 10517023 INFO @ Tue, 16 Jun 2020 08:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:14: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 08:44:14: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:14: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 08:44:14: #2 alternative fragment length(s) may be 3,66 bps INFO @ Tue, 16 Jun 2020 08:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.05_model.r WARNING @ Tue, 16 Jun 2020 08:44:14: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:14: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Tue, 16 Jun 2020 08:44:14: #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 08:44:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:15: 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 08:44:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.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 08:44:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:21: 5000000 INFO @ Tue, 16 Jun 2020 08:44:25: 1000000 INFO @ Tue, 16 Jun 2020 08:44:27: 6000000 INFO @ Tue, 16 Jun 2020 08:44:30: 2000000 INFO @ Tue, 16 Jun 2020 08:44:33: 7000000 INFO @ Tue, 16 Jun 2020 08:44:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:36: 3000000 INFO @ Tue, 16 Jun 2020 08:44:39: 8000000 INFO @ Tue, 16 Jun 2020 08:44:41: 4000000 INFO @ Tue, 16 Jun 2020 08:44:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.05_summits.bed INFO @ Tue, 16 Jun 2020 08:44:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2020 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:44:46: 9000000 INFO @ Tue, 16 Jun 2020 08:44:46: 5000000 INFO @ Tue, 16 Jun 2020 08:44:52: 6000000 INFO @ Tue, 16 Jun 2020 08:44:52: 10000000 INFO @ Tue, 16 Jun 2020 08:44:55: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:44:55: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:44:55: #1 total tags in treatment: 10517023 INFO @ Tue, 16 Jun 2020 08:44:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:55: #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 08:44:55: #1 tags after filtering in treatment: 10517023 INFO @ Tue, 16 Jun 2020 08:44:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:56: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 08:44:56: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:56: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 08:44:56: #2 alternative fragment length(s) may be 3,66 bps INFO @ Tue, 16 Jun 2020 08:44:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.10_model.r WARNING @ Tue, 16 Jun 2020 08:44:56: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:56: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Tue, 16 Jun 2020 08:44:56: #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 08:44:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:57: 7000000 INFO @ Tue, 16 Jun 2020 08:45:02: 8000000 INFO @ Tue, 16 Jun 2020 08:45:07: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:13: 10000000 INFO @ Tue, 16 Jun 2020 08:45:15: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:45:15: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:45:15: #1 total tags in treatment: 10517023 INFO @ Tue, 16 Jun 2020 08:45:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:15: #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 08:45:16: #1 tags after filtering in treatment: 10517023 INFO @ Tue, 16 Jun 2020 08:45:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:16: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 08:45:16: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:16: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 08:45:16: #2 alternative fragment length(s) may be 3,66 bps INFO @ Tue, 16 Jun 2020 08:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.20_model.r WARNING @ Tue, 16 Jun 2020 08:45:16: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:16: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Tue, 16 Jun 2020 08:45:16: #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 08:45:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.10_summits.bed INFO @ Tue, 16 Jun 2020 08:45:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:45:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942556/SRX3942556.20_summits.bed INFO @ Tue, 16 Jun 2020 08:45:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (186 records, 4 fields): 1 millis CompletedMACS2peakCalling