Job ID = 6627181 SRX = SRX8521308 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:27:46 prefetch.2.10.7: 1) Downloading 'SRR11978681'... 2020-07-14T01:27:46 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:28:45 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:28:45 prefetch.2.10.7: 'SRR11978681' is valid 2020-07-14T01:28:45 prefetch.2.10.7: 1) 'SRR11978681' was downloaded successfully 2020-07-14T01:28:45 prefetch.2.10.7: 'SRR11978681' has 0 unresolved dependencies Read 12186442 spots for SRR11978681/SRR11978681.sra Written 12186442 spots for SRR11978681/SRR11978681.sra 2020-07-14T01:29:41 prefetch.2.10.7: 1) Downloading 'SRR11978682'... 2020-07-14T01:29:41 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:31:20 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:31:20 prefetch.2.10.7: 'SRR11978682' is valid 2020-07-14T01:31:20 prefetch.2.10.7: 1) 'SRR11978682' was downloaded successfully 2020-07-14T01:31:20 prefetch.2.10.7: 'SRR11978682' has 0 unresolved dependencies Read 12202383 spots for SRR11978682/SRR11978682.sra Written 12202383 spots for SRR11978682/SRR11978682.sra 2020-07-14T01:32:22 prefetch.2.10.7: 1) Downloading 'SRR11978683'... 2020-07-14T01:32:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:33:46 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:33:47 prefetch.2.10.7: 'SRR11978683' is valid 2020-07-14T01:33:47 prefetch.2.10.7: 1) 'SRR11978683' was downloaded successfully 2020-07-14T01:33:47 prefetch.2.10.7: 'SRR11978683' has 0 unresolved dependencies Read 12137054 spots for SRR11978683/SRR11978683.sra Written 12137054 spots for SRR11978683/SRR11978683.sra 2020-07-14T01:34:48 prefetch.2.10.7: 1) Downloading 'SRR11978684'... 2020-07-14T01:34:48 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:36:16 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:36:17 prefetch.2.10.7: 'SRR11978684' is valid 2020-07-14T01:36:17 prefetch.2.10.7: 1) 'SRR11978684' was downloaded successfully 2020-07-14T01:36:17 prefetch.2.10.7: 'SRR11978684' has 0 unresolved dependencies Read 12328699 spots for SRR11978684/SRR11978684.sra Written 12328699 spots for SRR11978684/SRR11978684.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627436 ("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: 00:07:40 48854578 reads; of these: 48854578 (100.00%) were unpaired; of these: 44110956 (90.29%) aligned 0 times 3620865 (7.41%) aligned exactly 1 time 1122757 (2.30%) aligned >1 times 9.71% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 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] 880393 / 4743622 = 0.1856 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 10:46:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.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 10:46:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:46:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:47:06: 1000000 INFO @ Tue, 14 Jul 2020 10:47:15: 2000000 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 10:47:25: 3000000 INFO @ Tue, 14 Jul 2020 10:47:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.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 10:47:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:47:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:47:33: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 10:47:33: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 10:47:33: #1 total tags in treatment: 3863229 INFO @ Tue, 14 Jul 2020 10:47:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:47:33: #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 10:47:33: #1 tags after filtering in treatment: 3863229 INFO @ Tue, 14 Jul 2020 10:47:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:47:33: #1 finished! INFO @ Tue, 14 Jul 2020 10:47:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:47:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:47:33: 1000000 INFO @ Tue, 14 Jul 2020 10:47:33: #2 number of paired peaks: 622 WARNING @ Tue, 14 Jul 2020 10:47:33: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 14 Jul 2020 10:47:33: start model_add_line... INFO @ Tue, 14 Jul 2020 10:47:33: start X-correlation... INFO @ Tue, 14 Jul 2020 10:47:33: end of X-cor INFO @ Tue, 14 Jul 2020 10:47:33: #2 finished! INFO @ Tue, 14 Jul 2020 10:47:33: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:47:33: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 10:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.05_model.r WARNING @ Tue, 14 Jul 2020 10:47:33: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:47:33: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 10:47:33: #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 10:47:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:47:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:47:40: 2000000 INFO @ Tue, 14 Jul 2020 10:47:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:47:47: 3000000 INFO @ Tue, 14 Jul 2020 10:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:47:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.05_summits.bed INFO @ Tue, 14 Jul 2020 10:47:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1841 records, 4 fields): 4 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 10:47:54: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 10:47:54: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 10:47:54: #1 total tags in treatment: 3863229 INFO @ Tue, 14 Jul 2020 10:47:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:47:54: #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 10:47:54: #1 tags after filtering in treatment: 3863229 INFO @ Tue, 14 Jul 2020 10:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:47:54: #1 finished! INFO @ Tue, 14 Jul 2020 10:47:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:47:54: #2 number of paired peaks: 622 WARNING @ Tue, 14 Jul 2020 10:47:54: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 14 Jul 2020 10:47:54: start model_add_line... INFO @ Tue, 14 Jul 2020 10:47:54: start X-correlation... INFO @ Tue, 14 Jul 2020 10:47:54: end of X-cor INFO @ Tue, 14 Jul 2020 10:47:54: #2 finished! INFO @ Tue, 14 Jul 2020 10:47:54: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:47:54: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 10:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.10_model.r WARNING @ Tue, 14 Jul 2020 10:47:54: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:47:54: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 10:47:54: #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 10:47:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:47:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:47:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.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 10:47:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:47:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:48:03: 1000000 INFO @ Tue, 14 Jul 2020 10:48:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.10_summits.bed INFO @ Tue, 14 Jul 2020 10:48:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (810 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:48:10: 2000000 INFO @ Tue, 14 Jul 2020 10:48:17: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:48:23: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 10:48:23: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 10:48:23: #1 total tags in treatment: 3863229 INFO @ Tue, 14 Jul 2020 10:48:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:48:23: #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 10:48:23: #1 tags after filtering in treatment: 3863229 INFO @ Tue, 14 Jul 2020 10:48:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:48:23: #1 finished! INFO @ Tue, 14 Jul 2020 10:48:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:48:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:48:24: #2 number of paired peaks: 622 WARNING @ Tue, 14 Jul 2020 10:48:24: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 14 Jul 2020 10:48:24: start model_add_line... INFO @ Tue, 14 Jul 2020 10:48:24: start X-correlation... INFO @ Tue, 14 Jul 2020 10:48:24: end of X-cor INFO @ Tue, 14 Jul 2020 10:48:24: #2 finished! INFO @ Tue, 14 Jul 2020 10:48:24: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:48:24: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 10:48:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.20_model.r WARNING @ Tue, 14 Jul 2020 10:48:24: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:48:24: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 10:48:24: #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 10:48:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:48:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:48:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521308/SRX8521308.20_summits.bed INFO @ Tue, 14 Jul 2020 10:48:38: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 2 millis CompletedMACS2peakCalling