Job ID = 6627570 SRX = SRX8521406 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:02:03 prefetch.2.10.7: 1) Downloading 'SRR11978366'... 2020-07-14T03:02:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:03:16 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:03:17 prefetch.2.10.7: 'SRR11978366' is valid 2020-07-14T03:03:17 prefetch.2.10.7: 1) 'SRR11978366' was downloaded successfully 2020-07-14T03:03:17 prefetch.2.10.7: 'SRR11978366' has 0 unresolved dependencies Read 12923481 spots for SRR11978366/SRR11978366.sra Written 12923481 spots for SRR11978366/SRR11978366.sra 2020-07-14T03:04:13 prefetch.2.10.7: 1) Downloading 'SRR11978367'... 2020-07-14T03:04:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:05:14 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:05:15 prefetch.2.10.7: 'SRR11978367' is valid 2020-07-14T03:05:15 prefetch.2.10.7: 1) 'SRR11978367' was downloaded successfully 2020-07-14T03:05:15 prefetch.2.10.7: 'SRR11978367' has 0 unresolved dependencies Read 12646677 spots for SRR11978367/SRR11978367.sra Written 12646677 spots for SRR11978367/SRR11978367.sra 2020-07-14T03:06:10 prefetch.2.10.7: 1) Downloading 'SRR11978368'... 2020-07-14T03:06:10 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:12:55 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:12:56 prefetch.2.10.7: 'SRR11978368' is valid 2020-07-14T03:12:56 prefetch.2.10.7: 1) 'SRR11978368' was downloaded successfully 2020-07-14T03:12:56 prefetch.2.10.7: 'SRR11978368' has 0 unresolved dependencies Read 12584418 spots for SRR11978368/SRR11978368.sra Written 12584418 spots for SRR11978368/SRR11978368.sra 2020-07-14T03:14:20 prefetch.2.10.7: 1) Downloading 'SRR11978369'... 2020-07-14T03:14:20 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:15:42 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:15:43 prefetch.2.10.7: 'SRR11978369' is valid 2020-07-14T03:15:43 prefetch.2.10.7: 1) 'SRR11978369' was downloaded successfully 2020-07-14T03:15:43 prefetch.2.10.7: 'SRR11978369' has 0 unresolved dependencies Read 12770130 spots for SRR11978369/SRR11978369.sra Written 12770130 spots for SRR11978369/SRR11978369.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627781 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:57 50924706 reads; of these: 50924706 (100.00%) were unpaired; of these: 41273969 (81.05%) aligned 0 times 6733718 (13.22%) aligned exactly 1 time 2917019 (5.73%) aligned >1 times 18.95% overall alignment rate Time searching: 00:08:58 Overall time: 00:08:58 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] 1666563 / 9650737 = 0.1727 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 12:28:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.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 12:28:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:28:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:28:49: 1000000 INFO @ Tue, 14 Jul 2020 12:28:55: 2000000 INFO @ Tue, 14 Jul 2020 12:29:01: 3000000 INFO @ Tue, 14 Jul 2020 12:29:06: 4000000 INFO @ Tue, 14 Jul 2020 12:29:12: 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 12:29:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.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 12:29:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:29:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:29:18: 6000000 INFO @ Tue, 14 Jul 2020 12:29:20: 1000000 INFO @ Tue, 14 Jul 2020 12:29:24: 7000000 INFO @ Tue, 14 Jul 2020 12:29:26: 2000000 INFO @ Tue, 14 Jul 2020 12:29:30: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:29:30: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:29:30: #1 total tags in treatment: 7984174 INFO @ Tue, 14 Jul 2020 12:29:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:29:30: #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 12:29:31: #1 tags after filtering in treatment: 7984174 INFO @ Tue, 14 Jul 2020 12:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:29:31: #1 finished! INFO @ Tue, 14 Jul 2020 12:29:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:29:31: #2 number of paired peaks: 169 WARNING @ Tue, 14 Jul 2020 12:29:31: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 14 Jul 2020 12:29:31: start model_add_line... INFO @ Tue, 14 Jul 2020 12:29:31: start X-correlation... INFO @ Tue, 14 Jul 2020 12:29:31: end of X-cor INFO @ Tue, 14 Jul 2020 12:29:31: #2 finished! INFO @ Tue, 14 Jul 2020 12:29:31: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 12:29:31: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 14 Jul 2020 12:29:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.05_model.r WARNING @ Tue, 14 Jul 2020 12:29:31: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:29:31: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 14 Jul 2020 12:29:31: #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 12:29:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:29:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:29:32: 3000000 INFO @ Tue, 14 Jul 2020 12:29:38: 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 12:29:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.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 12:29:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:29:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:29:44: 5000000 INFO @ Tue, 14 Jul 2020 12:29:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:29:50: 1000000 INFO @ Tue, 14 Jul 2020 12:29:51: 6000000 INFO @ Tue, 14 Jul 2020 12:29:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:29:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:29:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.05_summits.bed INFO @ Tue, 14 Jul 2020 12:29:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1430 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:29:56: 2000000 INFO @ Tue, 14 Jul 2020 12:29:57: 7000000 INFO @ Tue, 14 Jul 2020 12:30:02: 3000000 INFO @ Tue, 14 Jul 2020 12:30:03: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:30:03: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:30:03: #1 total tags in treatment: 7984174 INFO @ Tue, 14 Jul 2020 12:30:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:30:03: #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 12:30:03: #1 tags after filtering in treatment: 7984174 INFO @ Tue, 14 Jul 2020 12:30:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:30:03: #1 finished! INFO @ Tue, 14 Jul 2020 12:30:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:30:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:30:04: #2 number of paired peaks: 169 WARNING @ Tue, 14 Jul 2020 12:30:04: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 14 Jul 2020 12:30:04: start model_add_line... INFO @ Tue, 14 Jul 2020 12:30:04: start X-correlation... INFO @ Tue, 14 Jul 2020 12:30:04: end of X-cor INFO @ Tue, 14 Jul 2020 12:30:04: #2 finished! INFO @ Tue, 14 Jul 2020 12:30:04: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 12:30:04: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 14 Jul 2020 12:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.10_model.r WARNING @ Tue, 14 Jul 2020 12:30:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:30:04: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 14 Jul 2020 12:30:04: #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 12:30:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:30:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:30:08: 4000000 INFO @ Tue, 14 Jul 2020 12:30:14: 5000000 INFO @ Tue, 14 Jul 2020 12:30:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:30:20: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:30:26: 7000000 INFO @ Tue, 14 Jul 2020 12:30:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:30:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:30:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.10_summits.bed INFO @ Tue, 14 Jul 2020 12:30:27: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (737 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:30:32: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:30:32: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:30:32: #1 total tags in treatment: 7984174 INFO @ Tue, 14 Jul 2020 12:30:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:30:32: #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 12:30:32: #1 tags after filtering in treatment: 7984174 INFO @ Tue, 14 Jul 2020 12:30:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:30:32: #1 finished! INFO @ Tue, 14 Jul 2020 12:30:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:30:33: #2 number of paired peaks: 169 WARNING @ Tue, 14 Jul 2020 12:30:33: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 14 Jul 2020 12:30:33: start model_add_line... INFO @ Tue, 14 Jul 2020 12:30:33: start X-correlation... INFO @ Tue, 14 Jul 2020 12:30:33: end of X-cor INFO @ Tue, 14 Jul 2020 12:30:33: #2 finished! INFO @ Tue, 14 Jul 2020 12:30:33: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 12:30:33: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 14 Jul 2020 12:30:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.20_model.r WARNING @ Tue, 14 Jul 2020 12:30:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:30:33: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 14 Jul 2020 12:30:33: #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 12:30:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:30:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:30:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:30:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:30:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:30:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521406/SRX8521406.20_summits.bed INFO @ Tue, 14 Jul 2020 12:30:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (306 records, 4 fields): 1 millis CompletedMACS2peakCalling