Job ID = 6455272 SRX = SRX287652 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:40 prefetch.2.10.7: 1) Downloading 'SRR869839'... 2020-06-21T09:48:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:51:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:51:14 prefetch.2.10.7: 'SRR869839' is valid 2020-06-21T09:51:14 prefetch.2.10.7: 1) 'SRR869839' was downloaded successfully Read 15682016 spots for SRR869839/SRR869839.sra Written 15682016 spots for SRR869839/SRR869839.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:32 15682016 reads; of these: 15682016 (100.00%) were unpaired; of these: 809996 (5.17%) aligned 0 times 11375387 (72.54%) aligned exactly 1 time 3496633 (22.30%) aligned >1 times 94.83% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2092555 / 14872020 = 0.1407 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 @ Sun, 21 Jun 2020 19:00:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.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 @ Sun, 21 Jun 2020 19:00:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:40: 1000000 INFO @ Sun, 21 Jun 2020 19:00:45: 2000000 INFO @ Sun, 21 Jun 2020 19:00:51: 3000000 INFO @ Sun, 21 Jun 2020 19:00:57: 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 @ Sun, 21 Jun 2020 19:01:03: 5000000 INFO @ Sun, 21 Jun 2020 19:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.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 @ Sun, 21 Jun 2020 19:01:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:09: 6000000 INFO @ Sun, 21 Jun 2020 19:01:10: 1000000 INFO @ Sun, 21 Jun 2020 19:01:16: 7000000 INFO @ Sun, 21 Jun 2020 19:01:17: 2000000 INFO @ Sun, 21 Jun 2020 19:01:22: 8000000 INFO @ Sun, 21 Jun 2020 19:01:24: 3000000 INFO @ Sun, 21 Jun 2020 19:01:29: 9000000 INFO @ Sun, 21 Jun 2020 19:01:30: 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 @ Sun, 21 Jun 2020 19:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.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 @ Sun, 21 Jun 2020 19:01:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:36: 10000000 INFO @ Sun, 21 Jun 2020 19:01:37: 5000000 INFO @ Sun, 21 Jun 2020 19:01:40: 1000000 INFO @ Sun, 21 Jun 2020 19:01:43: 11000000 INFO @ Sun, 21 Jun 2020 19:01:43: 6000000 INFO @ Sun, 21 Jun 2020 19:01:46: 2000000 INFO @ Sun, 21 Jun 2020 19:01:50: 12000000 INFO @ Sun, 21 Jun 2020 19:01:50: 7000000 INFO @ Sun, 21 Jun 2020 19:01:53: 3000000 INFO @ Sun, 21 Jun 2020 19:01:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:01:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:01:55: #1 total tags in treatment: 12779465 INFO @ Sun, 21 Jun 2020 19:01:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:01:56: #1 tags after filtering in treatment: 12779465 INFO @ Sun, 21 Jun 2020 19:01:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:56: #2 number of paired peaks: 527 WARNING @ Sun, 21 Jun 2020 19:01:56: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Sun, 21 Jun 2020 19:01:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:57: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:01:57: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:01:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.05_model.r WARNING @ Sun, 21 Jun 2020 19:01:57: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:01:57: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:01:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:01:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:57: 8000000 INFO @ Sun, 21 Jun 2020 19:01:59: 4000000 INFO @ Sun, 21 Jun 2020 19:02:03: 9000000 INFO @ Sun, 21 Jun 2020 19:02:05: 5000000 INFO @ Sun, 21 Jun 2020 19:02:10: 10000000 INFO @ Sun, 21 Jun 2020 19:02:12: 6000000 INFO @ Sun, 21 Jun 2020 19:02:17: 11000000 INFO @ Sun, 21 Jun 2020 19:02:18: 7000000 INFO @ Sun, 21 Jun 2020 19:02:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:24: 8000000 INFO @ Sun, 21 Jun 2020 19:02:24: 12000000 INFO @ Sun, 21 Jun 2020 19:02:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:30: #1 total tags in treatment: 12779465 INFO @ Sun, 21 Jun 2020 19:02:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:02:30: #1 tags after filtering in treatment: 12779465 INFO @ Sun, 21 Jun 2020 19:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:30: 9000000 INFO @ Sun, 21 Jun 2020 19:02:31: #2 number of paired peaks: 527 WARNING @ Sun, 21 Jun 2020 19:02:31: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Sun, 21 Jun 2020 19:02:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:31: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:02:31: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.10_model.r WARNING @ Sun, 21 Jun 2020 19:02:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:02:31: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:02:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:02:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.05_summits.bed INFO @ Sun, 21 Jun 2020 19:02:36: Done! pass1 - making usageList (505 chroms): 1 millis pass2 - checking and writing primary data (2097 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:02:36: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:02:43: 11000000 INFO @ Sun, 21 Jun 2020 19:02:49: 12000000 INFO @ Sun, 21 Jun 2020 19:02:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:54: #1 total tags in treatment: 12779465 INFO @ Sun, 21 Jun 2020 19:02:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:02:54: #1 tags after filtering in treatment: 12779465 INFO @ Sun, 21 Jun 2020 19:02:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:55: #2 number of paired peaks: 527 WARNING @ Sun, 21 Jun 2020 19:02:55: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Sun, 21 Jun 2020 19:02:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:55: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:02:55: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:02:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.20_model.r WARNING @ Sun, 21 Jun 2020 19:02:55: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:02:55: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:02:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:02:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.10_summits.bed INFO @ Sun, 21 Jun 2020 19:03:09: Done! pass1 - making usageList (430 chroms): 1 millis pass2 - checking and writing primary data (1394 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:03:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287652/SRX287652.20_summits.bed INFO @ Sun, 21 Jun 2020 19:03:33: Done! pass1 - making usageList (201 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 6 millis CompletedMACS2peakCalling