Job ID = 6369011 SRX = SRX982077 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:43:12 prefetch.2.10.7: 1) Downloading 'SRR1956557'... 2020-06-16T00:43:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:43:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:43:58 prefetch.2.10.7: 'SRR1956557' is valid 2020-06-16T00:43:58 prefetch.2.10.7: 1) 'SRR1956557' was downloaded successfully Read 4118030 spots for SRR1956557/SRR1956557.sra Written 4118030 spots for SRR1956557/SRR1956557.sra 2020-06-16T00:44:23 prefetch.2.10.7: 1) Downloading 'SRR1956558'... 2020-06-16T00:44:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:45:12 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:45:12 prefetch.2.10.7: 'SRR1956558' is valid 2020-06-16T00:45:12 prefetch.2.10.7: 1) 'SRR1956558' was downloaded successfully Read 5093036 spots for SRR1956558/SRR1956558.sra Written 5093036 spots for SRR1956558/SRR1956558.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: 00:02:00 9211066 reads; of these: 9211066 (100.00%) were unpaired; of these: 470322 (5.11%) aligned 0 times 7046925 (76.50%) aligned exactly 1 time 1693819 (18.39%) aligned >1 times 94.89% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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_rmdupse_core] 921120 / 8740744 = 0.1054 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 09:51:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.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 09:51:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:19: 1000000 INFO @ Tue, 16 Jun 2020 09:51:25: 2000000 INFO @ Tue, 16 Jun 2020 09:51:32: 3000000 INFO @ Tue, 16 Jun 2020 09:51:39: 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 @ Tue, 16 Jun 2020 09:51:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.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 09:51:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:46: 5000000 INFO @ Tue, 16 Jun 2020 09:51:47: 1000000 INFO @ Tue, 16 Jun 2020 09:51:53: 2000000 INFO @ Tue, 16 Jun 2020 09:51:53: 6000000 INFO @ Tue, 16 Jun 2020 09:51:58: 3000000 INFO @ Tue, 16 Jun 2020 09:52:01: 7000000 INFO @ Tue, 16 Jun 2020 09:52:03: 4000000 INFO @ Tue, 16 Jun 2020 09:52:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:52:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:52:06: #1 total tags in treatment: 7819624 INFO @ Tue, 16 Jun 2020 09:52:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:06: #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 09:52:06: #1 tags after filtering in treatment: 7819624 INFO @ Tue, 16 Jun 2020 09:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:07: #2 number of paired peaks: 468 WARNING @ Tue, 16 Jun 2020 09:52:07: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:07: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:52:07: #2 alternative fragment length(s) may be 4,63 bps INFO @ Tue, 16 Jun 2020 09:52:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.05_model.r WARNING @ Tue, 16 Jun 2020 09:52:07: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:52:07: #2 You may need to consider one of the other alternative d(s): 4,63 WARNING @ Tue, 16 Jun 2020 09:52:07: #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 09:52:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:09: 5000000 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 09:52:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.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 09:52:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:14: 6000000 INFO @ Tue, 16 Jun 2020 09:52:17: 1000000 INFO @ Tue, 16 Jun 2020 09:52:20: 7000000 INFO @ Tue, 16 Jun 2020 09:52:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:23: 2000000 INFO @ Tue, 16 Jun 2020 09:52:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:52:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:52:25: #1 total tags in treatment: 7819624 INFO @ Tue, 16 Jun 2020 09:52:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:25: #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 09:52:25: #1 tags after filtering in treatment: 7819624 INFO @ Tue, 16 Jun 2020 09:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:25: #2 number of paired peaks: 468 WARNING @ Tue, 16 Jun 2020 09:52:25: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:25: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:52:25: #2 alternative fragment length(s) may be 4,63 bps INFO @ Tue, 16 Jun 2020 09:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.10_model.r WARNING @ Tue, 16 Jun 2020 09:52:25: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:52:25: #2 You may need to consider one of the other alternative d(s): 4,63 WARNING @ Tue, 16 Jun 2020 09:52:25: #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 09:52:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:28: 3000000 INFO @ Tue, 16 Jun 2020 09:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.05_summits.bed INFO @ Tue, 16 Jun 2020 09:52:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1320 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:34: 4000000 INFO @ Tue, 16 Jun 2020 09:52:39: 5000000 INFO @ Tue, 16 Jun 2020 09:52:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:44: 6000000 INFO @ Tue, 16 Jun 2020 09:52:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.10_summits.bed INFO @ Tue, 16 Jun 2020 09:52:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:49: 7000000 INFO @ Tue, 16 Jun 2020 09:52:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:52:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:52:54: #1 total tags in treatment: 7819624 INFO @ Tue, 16 Jun 2020 09:52:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:54: #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 09:52:54: #1 tags after filtering in treatment: 7819624 INFO @ Tue, 16 Jun 2020 09:52:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:54: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:52:54: #2 number of paired peaks: 468 WARNING @ Tue, 16 Jun 2020 09:52:54: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:55: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:52:55: #2 alternative fragment length(s) may be 4,63 bps INFO @ Tue, 16 Jun 2020 09:52:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.20_model.r WARNING @ Tue, 16 Jun 2020 09:52:55: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:52:55: #2 You may need to consider one of the other alternative d(s): 4,63 WARNING @ Tue, 16 Jun 2020 09:52:55: #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 09:52:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982077/SRX982077.20_summits.bed INFO @ Tue, 16 Jun 2020 09:53:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。