Job ID = 6627182 SRX = SRX8521309 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:28:04 prefetch.2.10.7: 1) Downloading 'SRR11978685'... 2020-07-14T01:28:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:29:56 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:29:57 prefetch.2.10.7: 'SRR11978685' is valid 2020-07-14T01:29:57 prefetch.2.10.7: 1) 'SRR11978685' was downloaded successfully 2020-07-14T01:29:57 prefetch.2.10.7: 'SRR11978685' has 0 unresolved dependencies Read 12020371 spots for SRR11978685/SRR11978685.sra Written 12020371 spots for SRR11978685/SRR11978685.sra 2020-07-14T01:30:46 prefetch.2.10.7: 1) Downloading 'SRR11978686'... 2020-07-14T01:30:46 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:32:23 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:32:23 prefetch.2.10.7: 'SRR11978686' is valid 2020-07-14T01:32:23 prefetch.2.10.7: 1) 'SRR11978686' was downloaded successfully 2020-07-14T01:32:23 prefetch.2.10.7: 'SRR11978686' has 0 unresolved dependencies Read 12002892 spots for SRR11978686/SRR11978686.sra Written 12002892 spots for SRR11978686/SRR11978686.sra 2020-07-14T01:33:13 prefetch.2.10.7: 1) Downloading 'SRR11978687'... 2020-07-14T01:33:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:34:23 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:34:23 prefetch.2.10.7: 'SRR11978687' is valid 2020-07-14T01:34:23 prefetch.2.10.7: 1) 'SRR11978687' was downloaded successfully 2020-07-14T01:34:23 prefetch.2.10.7: 'SRR11978687' has 0 unresolved dependencies Read 11989748 spots for SRR11978687/SRR11978687.sra Written 11989748 spots for SRR11978687/SRR11978687.sra 2020-07-14T01:35:13 prefetch.2.10.7: 1) Downloading 'SRR11978688'... 2020-07-14T01:35:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:37:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:37:12 prefetch.2.10.7: 'SRR11978688' is valid 2020-07-14T01:37:12 prefetch.2.10.7: 1) 'SRR11978688' was downloaded successfully 2020-07-14T01:37:12 prefetch.2.10.7: 'SRR11978688' has 0 unresolved dependencies Read 12100014 spots for SRR11978688/SRR11978688.sra Written 12100014 spots for SRR11978688/SRR11978688.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627435 ("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: 00:06:45 48113025 reads; of these: 48113025 (100.00%) were unpaired; of these: 43752117 (90.94%) aligned 0 times 3320140 (6.90%) aligned exactly 1 time 1040768 (2.16%) aligned >1 times 9.06% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 826971 / 4360908 = 0.1896 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 10:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.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 10:46:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:46:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:46:43: 1000000 INFO @ Tue, 14 Jul 2020 10:46:48: 2000000 INFO @ Tue, 14 Jul 2020 10:46:54: 3000000 INFO @ Tue, 14 Jul 2020 10:46:57: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 10:46:57: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 10:46:57: #1 total tags in treatment: 3533937 INFO @ Tue, 14 Jul 2020 10:46:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:46:57: #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 10:46:57: #1 tags after filtering in treatment: 3533937 INFO @ Tue, 14 Jul 2020 10:46:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:46:57: #1 finished! INFO @ Tue, 14 Jul 2020 10:46:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:46:57: #2 number of paired peaks: 662 WARNING @ Tue, 14 Jul 2020 10:46:57: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Tue, 14 Jul 2020 10:46:57: start model_add_line... INFO @ Tue, 14 Jul 2020 10:46:57: start X-correlation... INFO @ Tue, 14 Jul 2020 10:46:57: end of X-cor INFO @ Tue, 14 Jul 2020 10:46:57: #2 finished! INFO @ Tue, 14 Jul 2020 10:46:57: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 10:46:57: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 10:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.05_model.r WARNING @ Tue, 14 Jul 2020 10:46:57: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:46:57: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 10:46:57: #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 10:46:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:47:05: #3 Call peaks for each chromosome... 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 10:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.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 10:47:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:47:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.05_summits.bed INFO @ Tue, 14 Jul 2020 10:47:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1805 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:47:13: 1000000 INFO @ Tue, 14 Jul 2020 10:47:18: 2000000 INFO @ Tue, 14 Jul 2020 10:47:24: 3000000 INFO @ Tue, 14 Jul 2020 10:47:27: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 10:47:27: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 10:47:27: #1 total tags in treatment: 3533937 INFO @ Tue, 14 Jul 2020 10:47:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:47:27: #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 10:47:27: #1 tags after filtering in treatment: 3533937 INFO @ Tue, 14 Jul 2020 10:47:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:47:27: #1 finished! INFO @ Tue, 14 Jul 2020 10:47:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:47:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:47:27: #2 number of paired peaks: 662 WARNING @ Tue, 14 Jul 2020 10:47:27: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Tue, 14 Jul 2020 10:47:27: start model_add_line... INFO @ Tue, 14 Jul 2020 10:47:27: start X-correlation... INFO @ Tue, 14 Jul 2020 10:47:27: end of X-cor INFO @ Tue, 14 Jul 2020 10:47:27: #2 finished! INFO @ Tue, 14 Jul 2020 10:47:27: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 10:47:27: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 10:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.10_model.r WARNING @ Tue, 14 Jul 2020 10:47:27: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:47:27: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 10:47:27: #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 10:47:27: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:47:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:47:34: #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 10:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.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 10:47:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:47:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:47:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:47:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:47:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.10_summits.bed INFO @ Tue, 14 Jul 2020 10:47:38: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (749 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:47:43: 1000000 INFO @ Tue, 14 Jul 2020 10:47:48: 2000000 INFO @ Tue, 14 Jul 2020 10:47:54: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:47:57: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 10:47:57: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 10:47:57: #1 total tags in treatment: 3533937 INFO @ Tue, 14 Jul 2020 10:47:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:47:57: #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 10:47:57: #1 tags after filtering in treatment: 3533937 INFO @ Tue, 14 Jul 2020 10:47:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:47:57: #1 finished! INFO @ Tue, 14 Jul 2020 10:47:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:47:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:47:57: #2 number of paired peaks: 662 WARNING @ Tue, 14 Jul 2020 10:47:57: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Tue, 14 Jul 2020 10:47:57: start model_add_line... INFO @ Tue, 14 Jul 2020 10:47:57: start X-correlation... INFO @ Tue, 14 Jul 2020 10:47:57: end of X-cor INFO @ Tue, 14 Jul 2020 10:47:57: #2 finished! INFO @ Tue, 14 Jul 2020 10:47:57: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 10:47:57: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 10:47:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.20_model.r WARNING @ Tue, 14 Jul 2020 10:47:57: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:47:57: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 10:47:57: #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 10:47:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:47:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:48:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521309/SRX8521309.20_summits.bed INFO @ Tue, 14 Jul 2020 10:48:09: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (174 records, 4 fields): 1 millis CompletedMACS2peakCalling