Job ID = 6627564 SRX = SRX8521402 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:00:33 prefetch.2.10.7: 1) Downloading 'SRR11978350'... 2020-07-14T03:00:33 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:01:39 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:01:39 prefetch.2.10.7: 'SRR11978350' is valid 2020-07-14T03:01:39 prefetch.2.10.7: 1) 'SRR11978350' was downloaded successfully 2020-07-14T03:01:39 prefetch.2.10.7: 'SRR11978350' has 0 unresolved dependencies Read 13682909 spots for SRR11978350/SRR11978350.sra Written 13682909 spots for SRR11978350/SRR11978350.sra 2020-07-14T03:02:46 prefetch.2.10.7: 1) Downloading 'SRR11978351'... 2020-07-14T03:02:46 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:03:53 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:03:54 prefetch.2.10.7: 'SRR11978351' is valid 2020-07-14T03:03:54 prefetch.2.10.7: 1) 'SRR11978351' was downloaded successfully 2020-07-14T03:03:54 prefetch.2.10.7: 'SRR11978351' has 0 unresolved dependencies Read 13433535 spots for SRR11978351/SRR11978351.sra Written 13433535 spots for SRR11978351/SRR11978351.sra 2020-07-14T03:04:55 prefetch.2.10.7: 1) Downloading 'SRR11978352'... 2020-07-14T03:04:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:06:49 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:06:50 prefetch.2.10.7: 'SRR11978352' is valid 2020-07-14T03:06:50 prefetch.2.10.7: 1) 'SRR11978352' was downloaded successfully 2020-07-14T03:06:50 prefetch.2.10.7: 'SRR11978352' has 0 unresolved dependencies Read 13757006 spots for SRR11978352/SRR11978352.sra Written 13757006 spots for SRR11978352/SRR11978352.sra 2020-07-14T03:07:56 prefetch.2.10.7: 1) Downloading 'SRR11978353'... 2020-07-14T03:07:56 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:09:06 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:09:06 prefetch.2.10.7: 'SRR11978353' is valid 2020-07-14T03:09:06 prefetch.2.10.7: 1) 'SRR11978353' was downloaded successfully 2020-07-14T03:09:06 prefetch.2.10.7: 'SRR11978353' has 0 unresolved dependencies Read 13689186 spots for SRR11978353/SRR11978353.sra Written 13689186 spots for SRR11978353/SRR11978353.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627755 ("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: 00:08:43 54562636 reads; of these: 54562636 (100.00%) were unpaired; of these: 48286465 (88.50%) aligned 0 times 4745769 (8.70%) aligned exactly 1 time 1530402 (2.80%) aligned >1 times 11.50% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 1077909 / 6276171 = 0.1717 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 12:21:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.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 12:21:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:21:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:21:32: 1000000 INFO @ Tue, 14 Jul 2020 12:21:40: 2000000 INFO @ Tue, 14 Jul 2020 12:21:48: 3000000 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 12:21:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.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 12:21:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:21:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:21:56: 4000000 INFO @ Tue, 14 Jul 2020 12:22:00: 1000000 INFO @ Tue, 14 Jul 2020 12:22:05: 5000000 INFO @ Tue, 14 Jul 2020 12:22:06: 2000000 INFO @ Tue, 14 Jul 2020 12:22:06: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 12:22:06: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 12:22:06: #1 total tags in treatment: 5198262 INFO @ Tue, 14 Jul 2020 12:22:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:06: #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 12:22:06: #1 tags after filtering in treatment: 5198262 INFO @ Tue, 14 Jul 2020 12:22:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:06: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:07: #2 number of paired peaks: 440 WARNING @ Tue, 14 Jul 2020 12:22:07: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Tue, 14 Jul 2020 12:22:07: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:07: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:07: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:07: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:07: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 12:22:07: #2 alternative fragment length(s) may be 57,509 bps INFO @ Tue, 14 Jul 2020 12:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.05_model.r WARNING @ Tue, 14 Jul 2020 12:22:07: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:07: #2 You may need to consider one of the other alternative d(s): 57,509 WARNING @ Tue, 14 Jul 2020 12:22:07: #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 12:22:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:22:12: 3000000 INFO @ Tue, 14 Jul 2020 12:22:18: 4000000 INFO @ Tue, 14 Jul 2020 12:22:19: #3 Call peaks for each chromosome... 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 12:22:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.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 12:22:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:22:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:22:24: 5000000 INFO @ Tue, 14 Jul 2020 12:22:25: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 12:22:25: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 12:22:25: #1 total tags in treatment: 5198262 INFO @ Tue, 14 Jul 2020 12:22:25: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:25: #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 12:22:25: #1 tags after filtering in treatment: 5198262 INFO @ Tue, 14 Jul 2020 12:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:25: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:25: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:26: #2 number of paired peaks: 440 WARNING @ Tue, 14 Jul 2020 12:22:26: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Tue, 14 Jul 2020 12:22:26: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:26: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:26: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:26: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:26: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 12:22:26: #2 alternative fragment length(s) may be 57,509 bps INFO @ Tue, 14 Jul 2020 12:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.10_model.r WARNING @ Tue, 14 Jul 2020 12:22:26: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:26: #2 You may need to consider one of the other alternative d(s): 57,509 WARNING @ Tue, 14 Jul 2020 12:22:26: #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 12:22:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.05_summits.bed INFO @ Tue, 14 Jul 2020 12:22:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1815 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:22:30: 1000000 INFO @ Tue, 14 Jul 2020 12:22:36: 2000000 INFO @ Tue, 14 Jul 2020 12:22:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:22:42: 3000000 INFO @ Tue, 14 Jul 2020 12:22:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:22:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:22:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.10_summits.bed INFO @ Tue, 14 Jul 2020 12:22:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:22:49: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:22:55: 5000000 INFO @ Tue, 14 Jul 2020 12:22:56: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 12:22:56: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 12:22:56: #1 total tags in treatment: 5198262 INFO @ Tue, 14 Jul 2020 12:22:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:56: #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 12:22:56: #1 tags after filtering in treatment: 5198262 INFO @ Tue, 14 Jul 2020 12:22:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:56: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:57: #2 number of paired peaks: 440 WARNING @ Tue, 14 Jul 2020 12:22:57: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Tue, 14 Jul 2020 12:22:57: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:57: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:57: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:57: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:57: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 12:22:57: #2 alternative fragment length(s) may be 57,509 bps INFO @ Tue, 14 Jul 2020 12:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.20_model.r WARNING @ Tue, 14 Jul 2020 12:22:57: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:57: #2 You may need to consider one of the other alternative d(s): 57,509 WARNING @ Tue, 14 Jul 2020 12:22:57: #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 12:22:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:23:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:23:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:23:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:23:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521402/SRX8521402.20_summits.bed INFO @ Tue, 14 Jul 2020 12:23:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (132 records, 4 fields): 1 millis CompletedMACS2peakCalling