Job ID = 6627297 SRX = SRX8521359 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:54:45 prefetch.2.10.7: 1) Downloading 'SRR11978090'... 2020-07-14T01:54:45 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:44 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:56:44 prefetch.2.10.7: 'SRR11978090' is valid 2020-07-14T01:56:44 prefetch.2.10.7: 1) 'SRR11978090' was downloaded successfully 2020-07-14T01:56:44 prefetch.2.10.7: 'SRR11978090' has 0 unresolved dependencies Read 11747678 spots for SRR11978090/SRR11978090.sra Written 11747678 spots for SRR11978090/SRR11978090.sra 2020-07-14T01:57:39 prefetch.2.10.7: 1) Downloading 'SRR11978091'... 2020-07-14T01:57:39 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:59:23 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:24 prefetch.2.10.7: 'SRR11978091' is valid 2020-07-14T01:59:24 prefetch.2.10.7: 1) 'SRR11978091' was downloaded successfully 2020-07-14T01:59:24 prefetch.2.10.7: 'SRR11978091' has 0 unresolved dependencies Read 11295982 spots for SRR11978091/SRR11978091.sra Written 11295982 spots for SRR11978091/SRR11978091.sra 2020-07-14T02:00:13 prefetch.2.10.7: 1) Downloading 'SRR11978092'... 2020-07-14T02:00:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:02:08 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:02:08 prefetch.2.10.7: 'SRR11978092' is valid 2020-07-14T02:02:08 prefetch.2.10.7: 1) 'SRR11978092' was downloaded successfully 2020-07-14T02:02:08 prefetch.2.10.7: 'SRR11978092' has 0 unresolved dependencies Read 11779872 spots for SRR11978092/SRR11978092.sra Written 11779872 spots for SRR11978092/SRR11978092.sra 2020-07-14T02:03:15 prefetch.2.10.7: 1) Downloading 'SRR11978093'... 2020-07-14T02:03:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:04:35 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:04:36 prefetch.2.10.7: 'SRR11978093' is valid 2020-07-14T02:04:36 prefetch.2.10.7: 1) 'SRR11978093' was downloaded successfully 2020-07-14T02:04:36 prefetch.2.10.7: 'SRR11978093' has 0 unresolved dependencies Read 11720810 spots for SRR11978093/SRR11978093.sra Written 11720810 spots for SRR11978093/SRR11978093.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627539 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:15 46544342 reads; of these: 46544342 (100.00%) were unpaired; of these: 40363903 (86.72%) aligned 0 times 4625329 (9.94%) aligned exactly 1 time 1555110 (3.34%) aligned >1 times 13.28% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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] 1263383 / 6180439 = 0.2044 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 11:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.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 11:16:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:16:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:16:25: 1000000 INFO @ Tue, 14 Jul 2020 11:16:32: 2000000 INFO @ Tue, 14 Jul 2020 11:16:38: 3000000 INFO @ Tue, 14 Jul 2020 11:16:45: 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, 14 Jul 2020 11:16:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.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 11:16:48: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:16:48: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:16:51: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 11:16:51: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 11:16:51: #1 total tags in treatment: 4917056 INFO @ Tue, 14 Jul 2020 11:16:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:16:51: #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 11:16:51: #1 tags after filtering in treatment: 4917056 INFO @ Tue, 14 Jul 2020 11:16:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:16:51: #1 finished! INFO @ Tue, 14 Jul 2020 11:16:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:16:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:16:52: #2 number of paired peaks: 674 WARNING @ Tue, 14 Jul 2020 11:16:52: 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 11:16:52: start model_add_line... INFO @ Tue, 14 Jul 2020 11:16:52: start X-correlation... INFO @ Tue, 14 Jul 2020 11:16:52: end of X-cor INFO @ Tue, 14 Jul 2020 11:16:52: #2 finished! INFO @ Tue, 14 Jul 2020 11:16:52: #2 predicted fragment length is 71 bps INFO @ Tue, 14 Jul 2020 11:16:52: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 14 Jul 2020 11:16:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.05_model.r WARNING @ Tue, 14 Jul 2020 11:16:52: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:16:52: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 14 Jul 2020 11:16:52: #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 11:16:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:16:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:16:55: 1000000 INFO @ Tue, 14 Jul 2020 11:17:02: 2000000 INFO @ Tue, 14 Jul 2020 11:17:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:17:09: 3000000 INFO @ Tue, 14 Jul 2020 11:17:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:17:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.05_summits.bed INFO @ Tue, 14 Jul 2020 11:17:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2709 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:17:15: 4000000 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 11:17:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.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 11:17:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:17:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:17:22: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 11:17:22: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 11:17:22: #1 total tags in treatment: 4917056 INFO @ Tue, 14 Jul 2020 11:17:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:17:22: #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 11:17:22: #1 tags after filtering in treatment: 4917056 INFO @ Tue, 14 Jul 2020 11:17:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:17:22: #1 finished! INFO @ Tue, 14 Jul 2020 11:17:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:17:22: #2 number of paired peaks: 674 WARNING @ Tue, 14 Jul 2020 11:17:22: 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 11:17:22: start model_add_line... INFO @ Tue, 14 Jul 2020 11:17:22: start X-correlation... INFO @ Tue, 14 Jul 2020 11:17:22: end of X-cor INFO @ Tue, 14 Jul 2020 11:17:22: #2 finished! INFO @ Tue, 14 Jul 2020 11:17:22: #2 predicted fragment length is 71 bps INFO @ Tue, 14 Jul 2020 11:17:22: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 14 Jul 2020 11:17:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.10_model.r WARNING @ Tue, 14 Jul 2020 11:17:22: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:17:22: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 14 Jul 2020 11:17:22: #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 11:17:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:17:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:17:28: 1000000 INFO @ Tue, 14 Jul 2020 11:17:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:17:38: 2000000 INFO @ Tue, 14 Jul 2020 11:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.10_summits.bed INFO @ Tue, 14 Jul 2020 11:17:41: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (987 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:17:47: 3000000 INFO @ Tue, 14 Jul 2020 11:17:56: 4000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:18:03: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 11:18:03: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 11:18:03: #1 total tags in treatment: 4917056 INFO @ Tue, 14 Jul 2020 11:18:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:18:03: #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 11:18:03: #1 tags after filtering in treatment: 4917056 INFO @ Tue, 14 Jul 2020 11:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:18:03: #1 finished! INFO @ Tue, 14 Jul 2020 11:18:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:18:04: #2 number of paired peaks: 674 WARNING @ Tue, 14 Jul 2020 11:18:04: 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 11:18:04: start model_add_line... INFO @ Tue, 14 Jul 2020 11:18:04: start X-correlation... INFO @ Tue, 14 Jul 2020 11:18:04: end of X-cor INFO @ Tue, 14 Jul 2020 11:18:04: #2 finished! INFO @ Tue, 14 Jul 2020 11:18:04: #2 predicted fragment length is 71 bps INFO @ Tue, 14 Jul 2020 11:18:04: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 14 Jul 2020 11:18:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.20_model.r WARNING @ Tue, 14 Jul 2020 11:18:04: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:18:04: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 14 Jul 2020 11:18:04: #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 11:18:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:18:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:18:17: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:18:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521359/SRX8521359.20_summits.bed INFO @ Tue, 14 Jul 2020 11:18:23: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 1 millis CompletedMACS2peakCalling