Job ID = 6627579 SRX = SRX8521413 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:04:02 prefetch.2.10.7: 1) Downloading 'SRR11978394'... 2020-07-14T03:04:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:05:29 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:05:30 prefetch.2.10.7: 'SRR11978394' is valid 2020-07-14T03:05:30 prefetch.2.10.7: 1) 'SRR11978394' was downloaded successfully 2020-07-14T03:05:30 prefetch.2.10.7: 'SRR11978394' has 0 unresolved dependencies Read 12307821 spots for SRR11978394/SRR11978394.sra Written 12307821 spots for SRR11978394/SRR11978394.sra 2020-07-14T03:06:25 prefetch.2.10.7: 1) Downloading 'SRR11978395'... 2020-07-14T03:06:25 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:07:56 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:07:56 prefetch.2.10.7: 'SRR11978395' is valid 2020-07-14T03:07:56 prefetch.2.10.7: 1) 'SRR11978395' was downloaded successfully 2020-07-14T03:07:56 prefetch.2.10.7: 'SRR11978395' has 0 unresolved dependencies Read 12135200 spots for SRR11978395/SRR11978395.sra Written 12135200 spots for SRR11978395/SRR11978395.sra 2020-07-14T03:08:50 prefetch.2.10.7: 1) Downloading 'SRR11978396'... 2020-07-14T03:08:50 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:10:50 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:10:51 prefetch.2.10.7: 'SRR11978396' is valid 2020-07-14T03:10:51 prefetch.2.10.7: 1) 'SRR11978396' was downloaded successfully 2020-07-14T03:10:51 prefetch.2.10.7: 'SRR11978396' has 0 unresolved dependencies Read 12266602 spots for SRR11978396/SRR11978396.sra Written 12266602 spots for SRR11978396/SRR11978396.sra 2020-07-14T03:11:47 prefetch.2.10.7: 1) Downloading 'SRR11978397'... 2020-07-14T03:11:47 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:13:43 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:13:44 prefetch.2.10.7: 'SRR11978397' is valid 2020-07-14T03:13:44 prefetch.2.10.7: 1) 'SRR11978397' was downloaded successfully 2020-07-14T03:13:44 prefetch.2.10.7: 'SRR11978397' has 0 unresolved dependencies Read 12184339 spots for SRR11978397/SRR11978397.sra Written 12184339 spots for SRR11978397/SRR11978397.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627766 ("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: 00:06:05 48893962 reads; of these: 48893962 (100.00%) were unpaired; of these: 45624646 (93.31%) aligned 0 times 2477701 (5.07%) aligned exactly 1 time 791615 (1.62%) aligned >1 times 6.69% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 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] 674242 / 3269316 = 0.2062 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 12:22:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.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 12:22:15: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:22:15: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:22:20: 1000000 INFO @ Tue, 14 Jul 2020 12:22:25: 2000000 INFO @ Tue, 14 Jul 2020 12:22:28: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:22:28: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:22:28: #1 total tags in treatment: 2595074 INFO @ Tue, 14 Jul 2020 12:22:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:28: #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 12:22:28: #1 tags after filtering in treatment: 2595074 INFO @ Tue, 14 Jul 2020 12:22:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:28: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:28: #2 number of paired peaks: 746 WARNING @ Tue, 14 Jul 2020 12:22:28: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Tue, 14 Jul 2020 12:22:28: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:29: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:29: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:29: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:29: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:22:29: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:22:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.05_model.r WARNING @ Tue, 14 Jul 2020 12:22:29: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:29: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:22:29: #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 12:22:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:22:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:22:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:22:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:22:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.05_summits.bed INFO @ Tue, 14 Jul 2020 12:22:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1387 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 12:22:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.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 12:22:45: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:22:45: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:22:50: 1000000 INFO @ Tue, 14 Jul 2020 12:22:55: 2000000 INFO @ Tue, 14 Jul 2020 12:22:58: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:22:58: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:22:58: #1 total tags in treatment: 2595074 INFO @ Tue, 14 Jul 2020 12:22:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:58: #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 12:22:58: #1 tags after filtering in treatment: 2595074 INFO @ Tue, 14 Jul 2020 12:22:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:58: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:58: #2 number of paired peaks: 746 WARNING @ Tue, 14 Jul 2020 12:22:58: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Tue, 14 Jul 2020 12:22:58: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:58: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:58: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:58: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:58: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:22:58: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:22:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.10_model.r WARNING @ Tue, 14 Jul 2020 12:22:58: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:58: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:22:58: #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 12:22:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:23:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:23:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.10_summits.bed INFO @ Tue, 14 Jul 2020 12:23:07: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (565 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 12:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.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 12:23:15: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:23:15: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:23:21: 1000000 INFO @ Tue, 14 Jul 2020 12:23:27: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:23:31: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:23:31: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:23:31: #1 total tags in treatment: 2595074 INFO @ Tue, 14 Jul 2020 12:23:31: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:23:31: #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 12:23:31: #1 tags after filtering in treatment: 2595074 INFO @ Tue, 14 Jul 2020 12:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:23:31: #1 finished! INFO @ Tue, 14 Jul 2020 12:23:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:23:31: #2 number of paired peaks: 746 WARNING @ Tue, 14 Jul 2020 12:23:31: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Tue, 14 Jul 2020 12:23:31: start model_add_line... INFO @ Tue, 14 Jul 2020 12:23:31: start X-correlation... INFO @ Tue, 14 Jul 2020 12:23:31: end of X-cor INFO @ Tue, 14 Jul 2020 12:23:31: #2 finished! INFO @ Tue, 14 Jul 2020 12:23:31: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:23:31: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.20_model.r WARNING @ Tue, 14 Jul 2020 12:23:31: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:23:31: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:23:31: #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 12:23:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:23:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:23:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:23:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:23:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521413/SRX8521413.20_summits.bed INFO @ Tue, 14 Jul 2020 12:23:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (112 records, 4 fields): 1 millis CompletedMACS2peakCalling