Job ID = 6627293 SRX = SRX8521356 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:53:26 prefetch.2.10.7: 1) Downloading 'SRR11978074'... 2020-07-14T01:53:26 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:54:00 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:54:00 prefetch.2.10.7: 'SRR11978074' is valid 2020-07-14T01:54:00 prefetch.2.10.7: 1) 'SRR11978074' was downloaded successfully 2020-07-14T01:54:00 prefetch.2.10.7: 'SRR11978074' has 0 unresolved dependencies Read 1693270 spots for SRR11978074/SRR11978074.sra Written 1693270 spots for SRR11978074/SRR11978074.sra 2020-07-14T01:54:21 prefetch.2.10.7: 1) Downloading 'SRR11978075'... 2020-07-14T01:54:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:54:45 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:54:45 prefetch.2.10.7: 'SRR11978075' is valid 2020-07-14T01:54:45 prefetch.2.10.7: 1) 'SRR11978075' was downloaded successfully 2020-07-14T01:54:45 prefetch.2.10.7: 'SRR11978075' has 0 unresolved dependencies Read 1676857 spots for SRR11978075/SRR11978075.sra Written 1676857 spots for SRR11978075/SRR11978075.sra 2020-07-14T01:55:05 prefetch.2.10.7: 1) Downloading 'SRR11978076'... 2020-07-14T01:55:05 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:55:35 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:55:35 prefetch.2.10.7: 'SRR11978076' is valid 2020-07-14T01:55:35 prefetch.2.10.7: 1) 'SRR11978076' was downloaded successfully 2020-07-14T01:55:35 prefetch.2.10.7: 'SRR11978076' has 0 unresolved dependencies Read 2892725 spots for SRR11978076/SRR11978076.sra Written 2892725 spots for SRR11978076/SRR11978076.sra 2020-07-14T01:55:59 prefetch.2.10.7: 1) Downloading 'SRR11978077'... 2020-07-14T01:55:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:56:32 prefetch.2.10.7: 'SRR11978077' is valid 2020-07-14T01:56:32 prefetch.2.10.7: 1) 'SRR11978077' was downloaded successfully 2020-07-14T01:56:32 prefetch.2.10.7: 'SRR11978077' has 0 unresolved dependencies Read 3292372 spots for SRR11978077/SRR11978077.sra Written 3292372 spots for SRR11978077/SRR11978077.sra 2020-07-14T01:56:53 prefetch.2.10.7: 1) Downloading 'SRR11978078'... 2020-07-14T01:56:53 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:13 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:58:13 prefetch.2.10.7: 'SRR11978078' is valid 2020-07-14T01:58:13 prefetch.2.10.7: 1) 'SRR11978078' was downloaded successfully 2020-07-14T01:58:13 prefetch.2.10.7: 'SRR11978078' has 0 unresolved dependencies Read 7656822 spots for SRR11978078/SRR11978078.sra Written 7656822 spots for SRR11978078/SRR11978078.sra 2020-07-14T01:58:52 prefetch.2.10.7: 1) Downloading 'SRR11978079'... 2020-07-14T01:58:52 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:00:02 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:00:02 prefetch.2.10.7: 'SRR11978079' is valid 2020-07-14T02:00:02 prefetch.2.10.7: 1) 'SRR11978079' was downloaded successfully 2020-07-14T02:00:02 prefetch.2.10.7: 'SRR11978079' has 0 unresolved dependencies Read 5564089 spots for SRR11978079/SRR11978079.sra Written 5564089 spots for SRR11978079/SRR11978079.sra 2020-07-14T02:00:42 prefetch.2.10.7: 1) Downloading 'SRR11978080'... 2020-07-14T02:00:42 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:01:26 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:01:26 prefetch.2.10.7: 'SRR11978080' is valid 2020-07-14T02:01:26 prefetch.2.10.7: 1) 'SRR11978080' was downloaded successfully 2020-07-14T02:01:26 prefetch.2.10.7: 'SRR11978080' has 0 unresolved dependencies Read 6567168 spots for SRR11978080/SRR11978080.sra Written 6567168 spots for SRR11978080/SRR11978080.sra 2020-07-14T02:02:02 prefetch.2.10.7: 1) Downloading 'SRR11978081'... 2020-07-14T02:02:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:02:40 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:02:40 prefetch.2.10.7: 'SRR11978081' is valid 2020-07-14T02:02:40 prefetch.2.10.7: 1) 'SRR11978081' was downloaded successfully 2020-07-14T02:02:40 prefetch.2.10.7: 'SRR11978081' has 0 unresolved dependencies Read 6219828 spots for SRR11978081/SRR11978081.sra Written 6219828 spots for SRR11978081/SRR11978081.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627520 ("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: 00:05:37 35563131 reads; of these: 35563131 (100.00%) were unpaired; of these: 29165380 (82.01%) aligned 0 times 4741213 (13.33%) aligned exactly 1 time 1656538 (4.66%) aligned >1 times 17.99% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 928441 / 6397751 = 0.1451 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 11:11:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.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 11:11:16: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:11:16: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:11:22: 1000000 INFO @ Tue, 14 Jul 2020 11:11:27: 2000000 INFO @ Tue, 14 Jul 2020 11:11:32: 3000000 INFO @ Tue, 14 Jul 2020 11:11:38: 4000000 INFO @ Tue, 14 Jul 2020 11:11:43: 5000000 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 11:11:46: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 11:11:46: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 11:11:46: #1 total tags in treatment: 5469310 INFO @ Tue, 14 Jul 2020 11:11:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:11:46: #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 11:11:46: #1 tags after filtering in treatment: 5469310 INFO @ Tue, 14 Jul 2020 11:11:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:11:46: #1 finished! INFO @ Tue, 14 Jul 2020 11:11:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:11:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:11:46: #2 number of paired peaks: 372 WARNING @ Tue, 14 Jul 2020 11:11:46: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 14 Jul 2020 11:11:46: start model_add_line... INFO @ Tue, 14 Jul 2020 11:11:46: start X-correlation... INFO @ Tue, 14 Jul 2020 11:11:46: end of X-cor INFO @ Tue, 14 Jul 2020 11:11:46: #2 finished! INFO @ Tue, 14 Jul 2020 11:11:46: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 11:11:46: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 14 Jul 2020 11:11:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.05_model.r WARNING @ Tue, 14 Jul 2020 11:11:46: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:11:46: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Tue, 14 Jul 2020 11:11:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:11:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:11:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:11:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.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 11:11:46: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:11:46: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:11:52: 1000000 INFO @ Tue, 14 Jul 2020 11:11:57: 2000000 INFO @ Tue, 14 Jul 2020 11:11:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:12:03: 3000000 INFO @ Tue, 14 Jul 2020 11:12:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:12:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:12:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.05_summits.bed INFO @ Tue, 14 Jul 2020 11:12:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1485 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:12:08: 4000000 INFO @ Tue, 14 Jul 2020 11:12:14: 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, 14 Jul 2020 11:12:16: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 11:12:16: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 11:12:16: #1 total tags in treatment: 5469310 INFO @ Tue, 14 Jul 2020 11:12:16: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:12:16: #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 11:12:16: #1 tags after filtering in treatment: 5469310 INFO @ Tue, 14 Jul 2020 11:12:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:12:16: #1 finished! INFO @ Tue, 14 Jul 2020 11:12:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:12:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:12:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.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 11:12:16: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:12:16: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:12:17: #2 number of paired peaks: 372 WARNING @ Tue, 14 Jul 2020 11:12:17: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 14 Jul 2020 11:12:17: start model_add_line... INFO @ Tue, 14 Jul 2020 11:12:17: start X-correlation... INFO @ Tue, 14 Jul 2020 11:12:17: end of X-cor INFO @ Tue, 14 Jul 2020 11:12:17: #2 finished! INFO @ Tue, 14 Jul 2020 11:12:17: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 11:12:17: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 14 Jul 2020 11:12:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.10_model.r WARNING @ Tue, 14 Jul 2020 11:12:17: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:12:17: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Tue, 14 Jul 2020 11:12:17: #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 11:12:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:12:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:12:22: 1000000 INFO @ Tue, 14 Jul 2020 11:12:27: 2000000 INFO @ Tue, 14 Jul 2020 11:12:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:12:32: 3000000 INFO @ Tue, 14 Jul 2020 11:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.10_summits.bed INFO @ Tue, 14 Jul 2020 11:12:33: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (549 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:12:38: 4000000 INFO @ Tue, 14 Jul 2020 11:12:43: 5000000 INFO @ Tue, 14 Jul 2020 11:12:45: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 11:12:45: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 11:12:45: #1 total tags in treatment: 5469310 INFO @ Tue, 14 Jul 2020 11:12:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:12:45: #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 11:12:45: #1 tags after filtering in treatment: 5469310 INFO @ Tue, 14 Jul 2020 11:12:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:12:45: #1 finished! INFO @ Tue, 14 Jul 2020 11:12:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:12:46: #2 number of paired peaks: 372 WARNING @ Tue, 14 Jul 2020 11:12:46: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 14 Jul 2020 11:12:46: start model_add_line... INFO @ Tue, 14 Jul 2020 11:12:46: start X-correlation... INFO @ Tue, 14 Jul 2020 11:12:46: end of X-cor INFO @ Tue, 14 Jul 2020 11:12:46: #2 finished! INFO @ Tue, 14 Jul 2020 11:12:46: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 11:12:46: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 14 Jul 2020 11:12:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.20_model.r WARNING @ Tue, 14 Jul 2020 11:12:46: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:12:46: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Tue, 14 Jul 2020 11:12:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:12:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:12:46: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:12:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521356/SRX8521356.20_summits.bed INFO @ Tue, 14 Jul 2020 11:13:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (122 records, 4 fields): 2 millis CompletedMACS2peakCalling