Job ID = 10166192 SRX = SRX7723712 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 48616499 spots for SRR11084668/SRR11084668.sra Written 48616499 spots for SRR11084668/SRR11084668.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166672 ("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: 00:19:27 48616499 reads; of these: 48616499 (100.00%) were unpaired; of these: 9394680 (19.32%) aligned 0 times 29175131 (60.01%) aligned exactly 1 time 10046688 (20.67%) aligned >1 times 80.68% overall alignment rate Time searching: 00:19:27 Overall time: 00:19:27 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_sort_core] merging from 16 files... [bam_rmdupse_core] 27975548 / 39221819 = 0.7133 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 @ Thu, 08 Oct 2020 21:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.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 @ Thu, 08 Oct 2020 21:06:01: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:06:01: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:06:08: 1000000 INFO @ Thu, 08 Oct 2020 21:06:14: 2000000 INFO @ Thu, 08 Oct 2020 21:06:20: 3000000 INFO @ Thu, 08 Oct 2020 21:06:26: 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 @ Thu, 08 Oct 2020 21:06:32: 5000000 INFO @ Thu, 08 Oct 2020 21:06:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.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 @ Thu, 08 Oct 2020 21:06:35: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:06:35: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:06:39: 6000000 INFO @ Thu, 08 Oct 2020 21:06:44: 1000000 INFO @ Thu, 08 Oct 2020 21:06:46: 7000000 INFO @ Thu, 08 Oct 2020 21:06:51: 2000000 INFO @ Thu, 08 Oct 2020 21:06:53: 8000000 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 @ Thu, 08 Oct 2020 21:06:58: 3000000 INFO @ Thu, 08 Oct 2020 21:07:01: 9000000 INFO @ Thu, 08 Oct 2020 21:07:05: 4000000 INFO @ Thu, 08 Oct 2020 21:07:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.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 @ Thu, 08 Oct 2020 21:07:06: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:07:06: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:07:08: 10000000 INFO @ Thu, 08 Oct 2020 21:07:12: 5000000 INFO @ Thu, 08 Oct 2020 21:07:15: 11000000 INFO @ Thu, 08 Oct 2020 21:07:17: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:07:17: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:07:17: #1 total tags in treatment: 11246271 INFO @ Thu, 08 Oct 2020 21:07:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:07:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:07:17: #1 tags after filtering in treatment: 11246271 INFO @ Thu, 08 Oct 2020 21:07:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:07:17: #1 finished! INFO @ Thu, 08 Oct 2020 21:07:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:07:17: 1000000 INFO @ Thu, 08 Oct 2020 21:07:18: #2 number of paired peaks: 445 WARNING @ Thu, 08 Oct 2020 21:07:18: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Thu, 08 Oct 2020 21:07:18: start model_add_line... INFO @ Thu, 08 Oct 2020 21:07:18: start X-correlation... INFO @ Thu, 08 Oct 2020 21:07:18: end of X-cor INFO @ Thu, 08 Oct 2020 21:07:18: #2 finished! INFO @ Thu, 08 Oct 2020 21:07:18: #2 predicted fragment length is 73 bps INFO @ Thu, 08 Oct 2020 21:07:18: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 08 Oct 2020 21:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05_model.r WARNING @ Thu, 08 Oct 2020 21:07:18: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:07:18: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 08 Oct 2020 21:07:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:07:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:07:20: 6000000 INFO @ Thu, 08 Oct 2020 21:07:25: 2000000 INFO @ Thu, 08 Oct 2020 21:07:27: 7000000 INFO @ Thu, 08 Oct 2020 21:07:32: 3000000 INFO @ Thu, 08 Oct 2020 21:07:34: 8000000 INFO @ Thu, 08 Oct 2020 21:07:39: 4000000 INFO @ Thu, 08 Oct 2020 21:07:41: 9000000 INFO @ Thu, 08 Oct 2020 21:07:42: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:07:46: 5000000 INFO @ Thu, 08 Oct 2020 21:07:49: 10000000 INFO @ Thu, 08 Oct 2020 21:07:53: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 21:07:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:07:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:07:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05_summits.bed INFO @ Thu, 08 Oct 2020 21:07:55: Done! INFO @ Thu, 08 Oct 2020 21:07:55: 11000000 INFO @ Thu, 08 Oct 2020 21:07:57: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:07:57: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:07:57: #1 total tags in treatment: 11246271 INFO @ Thu, 08 Oct 2020 21:07:57: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:07:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:07:57: #1 tags after filtering in treatment: 11246271 INFO @ Thu, 08 Oct 2020 21:07:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:07:57: #1 finished! INFO @ Thu, 08 Oct 2020 21:07:57: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:07:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:07:58: #2 number of paired peaks: 445 WARNING @ Thu, 08 Oct 2020 21:07:58: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Thu, 08 Oct 2020 21:07:58: start model_add_line... INFO @ Thu, 08 Oct 2020 21:07:58: start X-correlation... INFO @ Thu, 08 Oct 2020 21:07:58: end of X-cor INFO @ Thu, 08 Oct 2020 21:07:58: #2 finished! INFO @ Thu, 08 Oct 2020 21:07:58: #2 predicted fragment length is 73 bps INFO @ Thu, 08 Oct 2020 21:07:58: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 08 Oct 2020 21:07:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10_model.r WARNING @ Thu, 08 Oct 2020 21:07:58: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:07:58: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 08 Oct 2020 21:07:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:07:58: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:07:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:08:00: 7000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9740 records, 4 fields): 391 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:08:07: 8000000 INFO @ Thu, 08 Oct 2020 21:08:14: 9000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 21:08:20: 10000000 INFO @ Thu, 08 Oct 2020 21:08:22: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:08:27: 11000000 INFO @ Thu, 08 Oct 2020 21:08:28: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:08:28: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:08:28: #1 total tags in treatment: 11246271 INFO @ Thu, 08 Oct 2020 21:08:28: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:08:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:08:28: #1 tags after filtering in treatment: 11246271 INFO @ Thu, 08 Oct 2020 21:08:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:08:28: #1 finished! INFO @ Thu, 08 Oct 2020 21:08:28: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:08:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:08:29: #2 number of paired peaks: 445 WARNING @ Thu, 08 Oct 2020 21:08:29: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Thu, 08 Oct 2020 21:08:29: start model_add_line... INFO @ Thu, 08 Oct 2020 21:08:29: start X-correlation... INFO @ Thu, 08 Oct 2020 21:08:29: end of X-cor INFO @ Thu, 08 Oct 2020 21:08:29: #2 finished! INFO @ Thu, 08 Oct 2020 21:08:29: #2 predicted fragment length is 73 bps INFO @ Thu, 08 Oct 2020 21:08:29: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 08 Oct 2020 21:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20_model.r WARNING @ Thu, 08 Oct 2020 21:08:29: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:08:29: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 08 Oct 2020 21:08:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:08:29: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:08:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:08:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:08:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10_summits.bed INFO @ Thu, 08 Oct 2020 21:08:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2652 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:08:51: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:09:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20_peaks.xls INFO @ Thu, 08 Oct 2020 21:09:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:09:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20_summits.bed INFO @ Thu, 08 Oct 2020 21:09:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 2 millis CompletedMACS2peakCalling