Job ID = 5720717 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,031,498 reads read : 16,031,498 reads written : 16,031,498 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:05:37 16031498 reads; of these: 16031498 (100.00%) were unpaired; of these: 648011 (4.04%) aligned 0 times 8246616 (51.44%) aligned exactly 1 time 7136871 (44.52%) aligned >1 times 95.96% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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 8 files... [bam_rmdupse_core] 2128898 / 15383487 = 0.1384 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, 16 Apr 2020 01:22:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.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, 16 Apr 2020 01:22:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:22:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:22:41: 1000000 INFO @ Thu, 16 Apr 2020 01:22:46: 2000000 INFO @ Thu, 16 Apr 2020 01:22:51: 3000000 INFO @ Thu, 16 Apr 2020 01:22:56: 4000000 INFO @ Thu, 16 Apr 2020 01:23:01: 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 @ Thu, 16 Apr 2020 01:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.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, 16 Apr 2020 01:23:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:23:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:23:06: 6000000 INFO @ Thu, 16 Apr 2020 01:23:12: 1000000 INFO @ Thu, 16 Apr 2020 01:23:12: 7000000 INFO @ Thu, 16 Apr 2020 01:23:18: 8000000 INFO @ Thu, 16 Apr 2020 01:23:19: 2000000 INFO @ Thu, 16 Apr 2020 01:23:24: 9000000 INFO @ Thu, 16 Apr 2020 01:23:25: 3000000 INFO @ Thu, 16 Apr 2020 01:23:30: 10000000 INFO @ Thu, 16 Apr 2020 01:23:32: 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 @ Thu, 16 Apr 2020 01:23:36: 11000000 INFO @ Thu, 16 Apr 2020 01:23:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.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, 16 Apr 2020 01:23:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:23:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:23:39: 5000000 INFO @ Thu, 16 Apr 2020 01:23:42: 12000000 INFO @ Thu, 16 Apr 2020 01:23:42: 1000000 INFO @ Thu, 16 Apr 2020 01:23:45: 6000000 INFO @ Thu, 16 Apr 2020 01:23:47: 13000000 INFO @ Thu, 16 Apr 2020 01:23:48: 2000000 INFO @ Thu, 16 Apr 2020 01:23:49: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:23:49: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:23:49: #1 total tags in treatment: 13254589 INFO @ Thu, 16 Apr 2020 01:23:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:23:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:23:49: #1 tags after filtering in treatment: 13254589 INFO @ Thu, 16 Apr 2020 01:23:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:23:49: #1 finished! INFO @ Thu, 16 Apr 2020 01:23:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:23:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:23:50: #2 number of paired peaks: 688 WARNING @ Thu, 16 Apr 2020 01:23:50: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Thu, 16 Apr 2020 01:23:50: start model_add_line... INFO @ Thu, 16 Apr 2020 01:23:50: start X-correlation... INFO @ Thu, 16 Apr 2020 01:23:50: end of X-cor INFO @ Thu, 16 Apr 2020 01:23:50: #2 finished! INFO @ Thu, 16 Apr 2020 01:23:50: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 01:23:50: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 01:23:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.05_model.r WARNING @ Thu, 16 Apr 2020 01:23:50: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:23:50: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 01:23:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:23:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:23:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:23:52: 7000000 INFO @ Thu, 16 Apr 2020 01:23:54: 3000000 INFO @ Thu, 16 Apr 2020 01:23:59: 8000000 INFO @ Thu, 16 Apr 2020 01:24:00: 4000000 INFO @ Thu, 16 Apr 2020 01:24:05: 9000000 INFO @ Thu, 16 Apr 2020 01:24:06: 5000000 INFO @ Thu, 16 Apr 2020 01:24:11: 6000000 INFO @ Thu, 16 Apr 2020 01:24:12: 10000000 INFO @ Thu, 16 Apr 2020 01:24:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:24:17: 7000000 INFO @ Thu, 16 Apr 2020 01:24:19: 11000000 INFO @ Thu, 16 Apr 2020 01:24:23: 8000000 INFO @ Thu, 16 Apr 2020 01:24:26: 12000000 INFO @ Thu, 16 Apr 2020 01:24:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:24:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:24:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.05_summits.bed INFO @ Thu, 16 Apr 2020 01:24:29: Done! INFO @ Thu, 16 Apr 2020 01:24:29: 9000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3521 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:24:32: 13000000 INFO @ Thu, 16 Apr 2020 01:24:34: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:24:34: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:24:34: #1 total tags in treatment: 13254589 INFO @ Thu, 16 Apr 2020 01:24:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:24:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:24:34: #1 tags after filtering in treatment: 13254589 INFO @ Thu, 16 Apr 2020 01:24:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:24:34: #1 finished! INFO @ Thu, 16 Apr 2020 01:24:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:24:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:24:35: 10000000 INFO @ Thu, 16 Apr 2020 01:24:35: #2 number of paired peaks: 688 WARNING @ Thu, 16 Apr 2020 01:24:35: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Thu, 16 Apr 2020 01:24:35: start model_add_line... INFO @ Thu, 16 Apr 2020 01:24:35: start X-correlation... INFO @ Thu, 16 Apr 2020 01:24:35: end of X-cor INFO @ Thu, 16 Apr 2020 01:24:35: #2 finished! INFO @ Thu, 16 Apr 2020 01:24:35: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 01:24:35: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 01:24:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.10_model.r WARNING @ Thu, 16 Apr 2020 01:24:35: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:24:35: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 01:24:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:24:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:24:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:24:41: 11000000 INFO @ Thu, 16 Apr 2020 01:24:46: 12000000 INFO @ Thu, 16 Apr 2020 01:24:51: 13000000 INFO @ Thu, 16 Apr 2020 01:24:53: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:24:53: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:24:53: #1 total tags in treatment: 13254589 INFO @ Thu, 16 Apr 2020 01:24:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:24:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:24:53: #1 tags after filtering in treatment: 13254589 INFO @ Thu, 16 Apr 2020 01:24:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:24:53: #1 finished! INFO @ Thu, 16 Apr 2020 01:24:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:24:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:24:54: #2 number of paired peaks: 688 WARNING @ Thu, 16 Apr 2020 01:24:54: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Thu, 16 Apr 2020 01:24:54: start model_add_line... INFO @ Thu, 16 Apr 2020 01:24:54: start X-correlation... INFO @ Thu, 16 Apr 2020 01:24:54: end of X-cor INFO @ Thu, 16 Apr 2020 01:24:54: #2 finished! INFO @ Thu, 16 Apr 2020 01:24:54: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 01:24:54: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 01:24:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.20_model.r WARNING @ Thu, 16 Apr 2020 01:24:54: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:24:54: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 01:24:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:24:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:24:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:25:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:25:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:25:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:25:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.10_summits.bed INFO @ Thu, 16 Apr 2020 01:25:14: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1800 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:25:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:25:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:25:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:25:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158181/SRX4158181.20_summits.bed INFO @ Thu, 16 Apr 2020 01:25:32: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (927 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。