Job ID = 6627277 SRX = SRX8521344 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:48:15 prefetch.2.10.7: 1) Downloading 'SRR11978600'... 2020-07-14T01:48:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:49:17 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:49:17 prefetch.2.10.7: 'SRR11978600' is valid 2020-07-14T01:49:17 prefetch.2.10.7: 1) 'SRR11978600' was downloaded successfully 2020-07-14T01:49:17 prefetch.2.10.7: 'SRR11978600' has 0 unresolved dependencies Read 7431789 spots for SRR11978600/SRR11978600.sra Written 7431789 spots for SRR11978600/SRR11978600.sra 2020-07-14T01:49:55 prefetch.2.10.7: 1) Downloading 'SRR11978601'... 2020-07-14T01:49:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:50:53 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:50:54 prefetch.2.10.7: 'SRR11978601' is valid 2020-07-14T01:50:54 prefetch.2.10.7: 1) 'SRR11978601' was downloaded successfully 2020-07-14T01:50:54 prefetch.2.10.7: 'SRR11978601' has 0 unresolved dependencies Read 7274697 spots for SRR11978601/SRR11978601.sra Written 7274697 spots for SRR11978601/SRR11978601.sra 2020-07-14T01:51:28 prefetch.2.10.7: 1) Downloading 'SRR11978602'... 2020-07-14T01:51:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:52:18 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:52:18 prefetch.2.10.7: 'SRR11978602' is valid 2020-07-14T01:52:18 prefetch.2.10.7: 1) 'SRR11978602' was downloaded successfully 2020-07-14T01:52:18 prefetch.2.10.7: 'SRR11978602' has 0 unresolved dependencies Read 7551631 spots for SRR11978602/SRR11978602.sra Written 7551631 spots for SRR11978602/SRR11978602.sra 2020-07-14T01:52:59 prefetch.2.10.7: 1) Downloading 'SRR11978603'... 2020-07-14T01:52:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:54:03 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:54:03 prefetch.2.10.7: 'SRR11978603' is valid 2020-07-14T01:54:03 prefetch.2.10.7: 1) 'SRR11978603' was downloaded successfully 2020-07-14T01:54:03 prefetch.2.10.7: 'SRR11978603' has 0 unresolved dependencies Read 7557194 spots for SRR11978603/SRR11978603.sra Written 7557194 spots for SRR11978603/SRR11978603.sra 2020-07-14T01:54:43 prefetch.2.10.7: 1) Downloading 'SRR11978604'... 2020-07-14T01:54:43 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:55:15 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:55:16 prefetch.2.10.7: 'SRR11978604' is valid 2020-07-14T01:55:16 prefetch.2.10.7: 1) 'SRR11978604' was downloaded successfully 2020-07-14T01:55:16 prefetch.2.10.7: 'SRR11978604' has 0 unresolved dependencies Read 2773034 spots for SRR11978604/SRR11978604.sra Written 2773034 spots for SRR11978604/SRR11978604.sra 2020-07-14T01:55:36 prefetch.2.10.7: 1) Downloading 'SRR11978605'... 2020-07-14T01:55:36 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:13 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:56:13 prefetch.2.10.7: 'SRR11978605' is valid 2020-07-14T01:56:13 prefetch.2.10.7: 1) 'SRR11978605' was downloaded successfully 2020-07-14T01:56:13 prefetch.2.10.7: 'SRR11978605' has 0 unresolved dependencies Read 2684002 spots for SRR11978605/SRR11978605.sra Written 2684002 spots for SRR11978605/SRR11978605.sra 2020-07-14T01:56:37 prefetch.2.10.7: 1) Downloading 'SRR11978606'... 2020-07-14T01:56:37 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:57:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:57:32 prefetch.2.10.7: 'SRR11978606' is valid 2020-07-14T01:57:32 prefetch.2.10.7: 1) 'SRR11978606' was downloaded successfully 2020-07-14T01:57:32 prefetch.2.10.7: 'SRR11978606' has 0 unresolved dependencies Read 2864086 spots for SRR11978606/SRR11978606.sra Written 2864086 spots for SRR11978606/SRR11978606.sra 2020-07-14T01:57:52 prefetch.2.10.7: 1) Downloading 'SRR11978607'... 2020-07-14T01:57:52 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:59:02 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:02 prefetch.2.10.7: 'SRR11978607' is valid 2020-07-14T01:59:02 prefetch.2.10.7: 1) 'SRR11978607' was downloaded successfully 2020-07-14T01:59:02 prefetch.2.10.7: 'SRR11978607' has 0 unresolved dependencies Read 2792792 spots for SRR11978607/SRR11978607.sra Written 2792792 spots for SRR11978607/SRR11978607.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627513 ("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: 00:06:17 40929225 reads; of these: 40929225 (100.00%) were unpaired; of these: 35749470 (87.34%) aligned 0 times 3977743 (9.72%) aligned exactly 1 time 1202012 (2.94%) aligned >1 times 12.66% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 1138004 / 5179755 = 0.2197 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 11:07:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.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 11:07:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:07:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:07:50: 1000000 INFO @ Tue, 14 Jul 2020 11:07:57: 2000000 INFO @ Tue, 14 Jul 2020 11:08:04: 3000000 INFO @ Tue, 14 Jul 2020 11:08:11: 4000000 INFO @ Tue, 14 Jul 2020 11:08:11: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:08:11: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:08:11: #1 total tags in treatment: 4041751 INFO @ Tue, 14 Jul 2020 11:08:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:08:11: #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 11:08:11: #1 tags after filtering in treatment: 4041751 INFO @ Tue, 14 Jul 2020 11:08:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:08:11: #1 finished! INFO @ Tue, 14 Jul 2020 11:08:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:08:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:08:11: #2 number of paired peaks: 589 WARNING @ Tue, 14 Jul 2020 11:08:11: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Tue, 14 Jul 2020 11:08:11: start model_add_line... INFO @ Tue, 14 Jul 2020 11:08:12: start X-correlation... INFO @ Tue, 14 Jul 2020 11:08:12: end of X-cor INFO @ Tue, 14 Jul 2020 11:08:12: #2 finished! INFO @ Tue, 14 Jul 2020 11:08:12: #2 predicted fragment length is 70 bps INFO @ Tue, 14 Jul 2020 11:08:12: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 14 Jul 2020 11:08:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.05_model.r WARNING @ Tue, 14 Jul 2020 11:08:12: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:08:12: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 14 Jul 2020 11:08:12: #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 11:08:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:08:12: #3 Pre-compute pvalue-qvalue table... 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 11:08:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.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 11:08:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:08:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:08:20: 1000000 INFO @ Tue, 14 Jul 2020 11:08:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:08:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:08:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:08:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.05_summits.bed INFO @ Tue, 14 Jul 2020 11:08:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1608 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:08:27: 2000000 INFO @ Tue, 14 Jul 2020 11:08:34: 3000000 INFO @ Tue, 14 Jul 2020 11:08:40: 4000000 INFO @ Tue, 14 Jul 2020 11:08:40: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:08:40: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:08:40: #1 total tags in treatment: 4041751 INFO @ Tue, 14 Jul 2020 11:08:40: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:08:40: #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 11:08:41: #1 tags after filtering in treatment: 4041751 INFO @ Tue, 14 Jul 2020 11:08:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:08:41: #1 finished! INFO @ Tue, 14 Jul 2020 11:08:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:08:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:08:41: #2 number of paired peaks: 589 WARNING @ Tue, 14 Jul 2020 11:08:41: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Tue, 14 Jul 2020 11:08:41: start model_add_line... INFO @ Tue, 14 Jul 2020 11:08:41: start X-correlation... INFO @ Tue, 14 Jul 2020 11:08:41: end of X-cor INFO @ Tue, 14 Jul 2020 11:08:41: #2 finished! INFO @ Tue, 14 Jul 2020 11:08:41: #2 predicted fragment length is 70 bps INFO @ Tue, 14 Jul 2020 11:08:41: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 14 Jul 2020 11:08:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.10_model.r WARNING @ Tue, 14 Jul 2020 11:08:41: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:08:41: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 14 Jul 2020 11:08:41: #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 11:08:41: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:08:41: #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, 14 Jul 2020 11:08:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.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 11:08:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:08:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:08:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:08:50: 1000000 INFO @ Tue, 14 Jul 2020 11:08:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:08:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:08:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.10_summits.bed INFO @ Tue, 14 Jul 2020 11:08:54: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (586 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:08:56: 2000000 INFO @ Tue, 14 Jul 2020 11:09:02: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:09:08: 4000000 INFO @ Tue, 14 Jul 2020 11:09:08: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:09:08: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:09:08: #1 total tags in treatment: 4041751 INFO @ Tue, 14 Jul 2020 11:09:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:09:08: #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 11:09:08: #1 tags after filtering in treatment: 4041751 INFO @ Tue, 14 Jul 2020 11:09:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:09:08: #1 finished! INFO @ Tue, 14 Jul 2020 11:09:08: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:09:09: #2 number of paired peaks: 589 WARNING @ Tue, 14 Jul 2020 11:09:09: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Tue, 14 Jul 2020 11:09:09: start model_add_line... INFO @ Tue, 14 Jul 2020 11:09:09: start X-correlation... INFO @ Tue, 14 Jul 2020 11:09:09: end of X-cor INFO @ Tue, 14 Jul 2020 11:09:09: #2 finished! INFO @ Tue, 14 Jul 2020 11:09:09: #2 predicted fragment length is 70 bps INFO @ Tue, 14 Jul 2020 11:09:09: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 14 Jul 2020 11:09:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.20_model.r WARNING @ Tue, 14 Jul 2020 11:09:09: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:09:09: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 14 Jul 2020 11:09:09: #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 11:09:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:09:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:09:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:09:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:09:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:09:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521344/SRX8521344.20_summits.bed INFO @ Tue, 14 Jul 2020 11:09:22: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (162 records, 4 fields): 1 millis CompletedMACS2peakCalling