Job ID = 6455652 SRX = SRX287960 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:14:21 prefetch.2.10.7: 1) Downloading 'SRR870149'... 2020-06-21T10:14:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:17:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:17:04 prefetch.2.10.7: 1) 'SRR870149' was downloaded successfully Read 17133552 spots for SRR870149/SRR870149.sra Written 17133552 spots for SRR870149/SRR870149.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: 00:05:11 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 963611 (5.62%) aligned 0 times 11195708 (65.34%) aligned exactly 1 time 4974233 (29.03%) aligned >1 times 94.38% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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] 2735373 / 16169941 = 0.1692 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 19:27:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.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 19:27:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:30: 1000000 INFO @ Sun, 21 Jun 2020 19:27:37: 2000000 INFO @ Sun, 21 Jun 2020 19:27:43: 3000000 INFO @ Sun, 21 Jun 2020 19:27:50: 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 19:27:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.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 19:27:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:56: 5000000 INFO @ Sun, 21 Jun 2020 19:28:01: 1000000 INFO @ Sun, 21 Jun 2020 19:28:03: 6000000 INFO @ Sun, 21 Jun 2020 19:28:08: 2000000 INFO @ Sun, 21 Jun 2020 19:28:11: 7000000 INFO @ Sun, 21 Jun 2020 19:28:15: 3000000 INFO @ Sun, 21 Jun 2020 19:28:18: 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 @ Sun, 21 Jun 2020 19:28:21: 4000000 INFO @ Sun, 21 Jun 2020 19:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.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 19:28:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:25: 9000000 INFO @ Sun, 21 Jun 2020 19:28:28: 5000000 INFO @ Sun, 21 Jun 2020 19:28:30: 1000000 INFO @ Sun, 21 Jun 2020 19:28:33: 10000000 INFO @ Sun, 21 Jun 2020 19:28:35: 6000000 INFO @ Sun, 21 Jun 2020 19:28:37: 2000000 INFO @ Sun, 21 Jun 2020 19:28:40: 11000000 INFO @ Sun, 21 Jun 2020 19:28:43: 7000000 INFO @ Sun, 21 Jun 2020 19:28:45: 3000000 INFO @ Sun, 21 Jun 2020 19:28:48: 12000000 INFO @ Sun, 21 Jun 2020 19:28:49: 8000000 INFO @ Sun, 21 Jun 2020 19:28:51: 4000000 INFO @ Sun, 21 Jun 2020 19:28:55: 13000000 INFO @ Sun, 21 Jun 2020 19:28:56: 9000000 INFO @ Sun, 21 Jun 2020 19:28:58: 5000000 INFO @ Sun, 21 Jun 2020 19:28:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:59: #1 total tags in treatment: 13434568 INFO @ Sun, 21 Jun 2020 19:28:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:59: #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 19:28:59: #1 tags after filtering in treatment: 13434568 INFO @ Sun, 21 Jun 2020 19:28:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:00: #2 number of paired peaks: 445 WARNING @ Sun, 21 Jun 2020 19:29:00: 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 @ Sun, 21 Jun 2020 19:29:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:00: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:29:00: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.05_model.r WARNING @ Sun, 21 Jun 2020 19:29:00: #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 19:29:00: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:29:00: #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 19:29:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:03: 10000000 INFO @ Sun, 21 Jun 2020 19:29:05: 6000000 INFO @ Sun, 21 Jun 2020 19:29:10: 11000000 INFO @ Sun, 21 Jun 2020 19:29:12: 7000000 INFO @ Sun, 21 Jun 2020 19:29:17: 12000000 INFO @ Sun, 21 Jun 2020 19:29:19: 8000000 INFO @ Sun, 21 Jun 2020 19:29:24: 13000000 INFO @ Sun, 21 Jun 2020 19:29:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:26: 9000000 INFO @ Sun, 21 Jun 2020 19:29:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:27: #1 total tags in treatment: 13434568 INFO @ Sun, 21 Jun 2020 19:29:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:27: #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 19:29:28: #1 tags after filtering in treatment: 13434568 INFO @ Sun, 21 Jun 2020 19:29:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:29: #2 number of paired peaks: 445 WARNING @ Sun, 21 Jun 2020 19:29:29: 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 @ Sun, 21 Jun 2020 19:29:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:29: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:29:29: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:29:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.10_model.r WARNING @ Sun, 21 Jun 2020 19:29:29: #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 19:29:29: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:29:29: #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 19:29:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:32: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:29:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.05_summits.bed INFO @ Sun, 21 Jun 2020 19:29:38: Done! pass1 - making usageList (615 chroms): 2 millis pass2 - checking and writing primary data (2450 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:29:39: 11000000 INFO @ Sun, 21 Jun 2020 19:29:46: 12000000 INFO @ Sun, 21 Jun 2020 19:29:52: 13000000 INFO @ Sun, 21 Jun 2020 19:29:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:55: #1 total tags in treatment: 13434568 INFO @ Sun, 21 Jun 2020 19:29:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:55: #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 19:29:56: #1 tags after filtering in treatment: 13434568 INFO @ Sun, 21 Jun 2020 19:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:57: #2 number of paired peaks: 445 WARNING @ Sun, 21 Jun 2020 19:29:57: 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 @ Sun, 21 Jun 2020 19:29:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:57: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:29:57: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:29:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.20_model.r WARNING @ Sun, 21 Jun 2020 19:29:57: #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 19:29:57: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:29:57: #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 19:29:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:30:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.10_summits.bed INFO @ Sun, 21 Jun 2020 19:30:07: Done! pass1 - making usageList (507 chroms): 1 millis pass2 - checking and writing primary data (1746 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287960/SRX287960.20_summits.bed INFO @ Sun, 21 Jun 2020 19:30:35: Done! pass1 - making usageList (273 chroms): 1 millis pass2 - checking and writing primary data (583 records, 4 fields): 8 millis CompletedMACS2peakCalling