Job ID = 6366256 SRX = SRX094514 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:42:52 prefetch.2.10.7: 1) Downloading 'SRR340088'... 2020-06-15T22:42:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:59 prefetch.2.10.7: 'SRR340088' is valid 2020-06-15T22:43:59 prefetch.2.10.7: 1) 'SRR340088' was downloaded successfully Read 17659150 spots for SRR340088/SRR340088.sra Written 17659150 spots for SRR340088/SRR340088.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: 00:03:24 17659150 reads; of these: 17659150 (100.00%) were unpaired; of these: 1070282 (6.06%) aligned 0 times 13655793 (77.33%) aligned exactly 1 time 2933075 (16.61%) aligned >1 times 93.94% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 8208698 / 16588868 = 0.4948 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 07:51:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.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 07:51:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:59: 1000000 INFO @ Tue, 16 Jun 2020 07:52:05: 2000000 INFO @ Tue, 16 Jun 2020 07:52:12: 3000000 INFO @ Tue, 16 Jun 2020 07:52:18: 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 07:52:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.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 07:52:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:25: 5000000 INFO @ Tue, 16 Jun 2020 07:52:30: 1000000 INFO @ Tue, 16 Jun 2020 07:52:32: 6000000 INFO @ Tue, 16 Jun 2020 07:52:37: 2000000 INFO @ Tue, 16 Jun 2020 07:52:39: 7000000 INFO @ Tue, 16 Jun 2020 07:52:45: 3000000 INFO @ Tue, 16 Jun 2020 07:52:46: 8000000 INFO @ Tue, 16 Jun 2020 07:52:48: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:52:48: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:52:48: #1 total tags in treatment: 8380170 INFO @ Tue, 16 Jun 2020 07:52:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:48: #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 07:52:49: #1 tags after filtering in treatment: 8380170 INFO @ Tue, 16 Jun 2020 07:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:49: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:49: #2 number of paired peaks: 582 WARNING @ Tue, 16 Jun 2020 07:52:49: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:49: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 07:52:49: #2 alternative fragment length(s) may be 3,38,566 bps INFO @ Tue, 16 Jun 2020 07:52:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.05_model.r WARNING @ Tue, 16 Jun 2020 07:52:49: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:49: #2 You may need to consider one of the other alternative d(s): 3,38,566 WARNING @ Tue, 16 Jun 2020 07:52:49: #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 07:52:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:49: #3 Pre-compute pvalue-qvalue table... 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 07:52:52: 4000000 INFO @ Tue, 16 Jun 2020 07:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.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 07:52:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:59: 5000000 INFO @ Tue, 16 Jun 2020 07:53:00: 1000000 INFO @ Tue, 16 Jun 2020 07:53:06: 6000000 INFO @ Tue, 16 Jun 2020 07:53:06: 2000000 INFO @ Tue, 16 Jun 2020 07:53:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:13: 7000000 INFO @ Tue, 16 Jun 2020 07:53:13: 3000000 INFO @ Tue, 16 Jun 2020 07:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (851 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:20: 8000000 INFO @ Tue, 16 Jun 2020 07:53:20: 4000000 INFO @ Tue, 16 Jun 2020 07:53:22: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:53:22: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:53:22: #1 total tags in treatment: 8380170 INFO @ Tue, 16 Jun 2020 07:53:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:22: #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 07:53:23: #1 tags after filtering in treatment: 8380170 INFO @ Tue, 16 Jun 2020 07:53:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:23: #2 number of paired peaks: 582 WARNING @ Tue, 16 Jun 2020 07:53:23: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:23: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 07:53:23: #2 alternative fragment length(s) may be 3,38,566 bps INFO @ Tue, 16 Jun 2020 07:53:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.10_model.r WARNING @ Tue, 16 Jun 2020 07:53:23: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:23: #2 You may need to consider one of the other alternative d(s): 3,38,566 WARNING @ Tue, 16 Jun 2020 07:53:23: #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 07:53:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:26: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:53:32: 6000000 INFO @ Tue, 16 Jun 2020 07:53:38: 7000000 INFO @ Tue, 16 Jun 2020 07:53:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:43: 8000000 INFO @ Tue, 16 Jun 2020 07:53:45: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:53:45: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:53:45: #1 total tags in treatment: 8380170 INFO @ Tue, 16 Jun 2020 07:53:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:45: #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 07:53:45: #1 tags after filtering in treatment: 8380170 INFO @ Tue, 16 Jun 2020 07:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:45: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:46: #2 number of paired peaks: 582 WARNING @ Tue, 16 Jun 2020 07:53:46: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:46: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:46: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:46: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:46: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:46: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 07:53:46: #2 alternative fragment length(s) may be 3,38,566 bps INFO @ Tue, 16 Jun 2020 07:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.20_model.r WARNING @ Tue, 16 Jun 2020 07:53:46: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:46: #2 You may need to consider one of the other alternative d(s): 3,38,566 WARNING @ Tue, 16 Jun 2020 07:53:46: #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 07:53:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.10_summits.bed INFO @ Tue, 16 Jun 2020 07:53:50: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (514 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX094514/SRX094514.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (175 records, 4 fields): 1 millis CompletedMACS2peakCalling