Job ID = 6627582 SRX = SRX8521415 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:04:47 prefetch.2.10.7: 1) Downloading 'SRR11978402'... 2020-07-14T03:04:47 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:06:08 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:06:09 prefetch.2.10.7: 'SRR11978402' is valid 2020-07-14T03:06:09 prefetch.2.10.7: 1) 'SRR11978402' was downloaded successfully 2020-07-14T03:06:09 prefetch.2.10.7: 'SRR11978402' has 0 unresolved dependencies Read 12105732 spots for SRR11978402/SRR11978402.sra Written 12105732 spots for SRR11978402/SRR11978402.sra 2020-07-14T03:07:07 prefetch.2.10.7: 1) Downloading 'SRR11978403'... 2020-07-14T03:07:07 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:08:28 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:08:28 prefetch.2.10.7: 'SRR11978403' is valid 2020-07-14T03:08:28 prefetch.2.10.7: 1) 'SRR11978403' was downloaded successfully 2020-07-14T03:08:28 prefetch.2.10.7: 'SRR11978403' has 0 unresolved dependencies Read 11873490 spots for SRR11978403/SRR11978403.sra Written 11873490 spots for SRR11978403/SRR11978403.sra 2020-07-14T03:09:21 prefetch.2.10.7: 1) Downloading 'SRR11978404'... 2020-07-14T03:09:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:10:41 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:10:42 prefetch.2.10.7: 'SRR11978404' is valid 2020-07-14T03:10:42 prefetch.2.10.7: 1) 'SRR11978404' was downloaded successfully 2020-07-14T03:10:42 prefetch.2.10.7: 'SRR11978404' has 0 unresolved dependencies Read 12045473 spots for SRR11978404/SRR11978404.sra Written 12045473 spots for SRR11978404/SRR11978404.sra 2020-07-14T03:11:36 prefetch.2.10.7: 1) Downloading 'SRR11978405'... 2020-07-14T03:11:36 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:13:01 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:13:02 prefetch.2.10.7: 'SRR11978405' is valid 2020-07-14T03:13:02 prefetch.2.10.7: 1) 'SRR11978405' was downloaded successfully 2020-07-14T03:13:02 prefetch.2.10.7: 'SRR11978405' has 0 unresolved dependencies Read 11774893 spots for SRR11978405/SRR11978405.sra Written 11774893 spots for SRR11978405/SRR11978405.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627760 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:05 47799588 reads; of these: 47799588 (100.00%) were unpaired; of these: 44605339 (93.32%) aligned 0 times 2411853 (5.05%) aligned exactly 1 time 782396 (1.64%) aligned >1 times 6.68% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 660344 / 3194249 = 0.2067 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, 14 Jul 2020 12:21:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 12:21:31: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:21:31: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:21:36: 1000000 INFO @ Tue, 14 Jul 2020 12:21:42: 2000000 INFO @ Tue, 14 Jul 2020 12:21:45: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 12:21:45: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 12:21:45: #1 total tags in treatment: 2533905 INFO @ Tue, 14 Jul 2020 12:21:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:21:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:21:45: #1 tags after filtering in treatment: 2533905 INFO @ Tue, 14 Jul 2020 12:21:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:21:45: #1 finished! INFO @ Tue, 14 Jul 2020 12:21:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:21:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:21:45: #2 number of paired peaks: 674 WARNING @ Tue, 14 Jul 2020 12:21:45: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Tue, 14 Jul 2020 12:21:45: start model_add_line... INFO @ Tue, 14 Jul 2020 12:21:45: start X-correlation... INFO @ Tue, 14 Jul 2020 12:21:45: end of X-cor INFO @ Tue, 14 Jul 2020 12:21:45: #2 finished! INFO @ Tue, 14 Jul 2020 12:21:45: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 12:21:45: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 12:21:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.05_model.r WARNING @ Tue, 14 Jul 2020 12:21:45: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:21:45: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 12:21:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:21:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:21:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:21:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:21:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:21:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:21:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.05_summits.bed INFO @ Tue, 14 Jul 2020 12:21:53: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1118 records, 4 fields): 3 millis CompletedMACS2peakCalling 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, 14 Jul 2020 12:22:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 12:22:01: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:22:01: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:22:06: 1000000 INFO @ Tue, 14 Jul 2020 12:22:12: 2000000 INFO @ Tue, 14 Jul 2020 12:22:15: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 12:22:15: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 12:22:15: #1 total tags in treatment: 2533905 INFO @ Tue, 14 Jul 2020 12:22:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:22:15: #1 tags after filtering in treatment: 2533905 INFO @ Tue, 14 Jul 2020 12:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:15: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:15: #2 number of paired peaks: 674 WARNING @ Tue, 14 Jul 2020 12:22:15: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Tue, 14 Jul 2020 12:22:15: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:15: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:15: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:15: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:15: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 12:22:15: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 12:22:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.10_model.r WARNING @ Tue, 14 Jul 2020 12:22:15: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:15: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 12:22:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:22:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:22:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.10_summits.bed INFO @ Tue, 14 Jul 2020 12:22:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (443 records, 4 fields): 1 millis CompletedMACS2peakCalling 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, 14 Jul 2020 12:22:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 12:22:31: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:22:31: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:22:36: 1000000 INFO @ Tue, 14 Jul 2020 12:22:42: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:22:45: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 12:22:45: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 12:22:45: #1 total tags in treatment: 2533905 INFO @ Tue, 14 Jul 2020 12:22:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:22:45: #1 tags after filtering in treatment: 2533905 INFO @ Tue, 14 Jul 2020 12:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:45: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:45: #2 number of paired peaks: 674 WARNING @ Tue, 14 Jul 2020 12:22:45: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Tue, 14 Jul 2020 12:22:45: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:45: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:45: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:45: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:45: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 12:22:45: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 12:22:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.20_model.r WARNING @ Tue, 14 Jul 2020 12:22:45: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:45: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 12:22:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:22:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:22:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:22:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:22:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:22:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521415/SRX8521415.20_summits.bed INFO @ Tue, 14 Jul 2020 12:22:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (95 records, 4 fields): 2 millis CompletedMACS2peakCalling