Job ID = 6456667 SRX = SRX3937194 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:57:16 prefetch.2.10.7: 1) Downloading 'SRR7004614'... 2020-06-21T10:57:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:58:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:58:45 prefetch.2.10.7: 'SRR7004614' is valid 2020-06-21T10:58:45 prefetch.2.10.7: 1) 'SRR7004614' was downloaded successfully 2020-06-21T10:58:45 prefetch.2.10.7: 'SRR7004614' has 0 unresolved dependencies Read 3384442 spots for SRR7004614/SRR7004614.sra Written 3384442 spots for SRR7004614/SRR7004614.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:36 3384442 reads; of these: 3384442 (100.00%) were unpaired; of these: 794389 (23.47%) aligned 0 times 1777671 (52.52%) aligned exactly 1 time 812382 (24.00%) aligned >1 times 76.53% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 167456 / 2590053 = 0.0647 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 20:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.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 20:02:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:02:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:02:16: 1000000 INFO @ Sun, 21 Jun 2020 20:02:23: 2000000 INFO @ Sun, 21 Jun 2020 20:02:26: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:02:26: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:02:26: #1 total tags in treatment: 2422597 INFO @ Sun, 21 Jun 2020 20:02:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:02:26: #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 20:02:27: #1 tags after filtering in treatment: 2422564 INFO @ Sun, 21 Jun 2020 20:02:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:02:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:02:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:02:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:02:27: #2 number of paired peaks: 737 WARNING @ Sun, 21 Jun 2020 20:02:27: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Sun, 21 Jun 2020 20:02:27: start model_add_line... INFO @ Sun, 21 Jun 2020 20:02:27: start X-correlation... INFO @ Sun, 21 Jun 2020 20:02:27: end of X-cor INFO @ Sun, 21 Jun 2020 20:02:27: #2 finished! INFO @ Sun, 21 Jun 2020 20:02:27: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 20:02:27: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 20:02:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.05_model.r WARNING @ Sun, 21 Jun 2020 20:02:27: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:02:27: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 21 Jun 2020 20:02:27: #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 20:02:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:02:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:02:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:02:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:02:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.05_summits.bed INFO @ Sun, 21 Jun 2020 20:02:36: Done! pass1 - making usageList (509 chroms): 2 millis pass2 - checking and writing primary data (1056 records, 4 fields): 14 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 @ Sun, 21 Jun 2020 20:02:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.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 20:02:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:02:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:02:47: 1000000 INFO @ Sun, 21 Jun 2020 20:02:54: 2000000 INFO @ Sun, 21 Jun 2020 20:02:57: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:02:57: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:02:57: #1 total tags in treatment: 2422597 INFO @ Sun, 21 Jun 2020 20:02:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:02:57: #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 20:02:57: #1 tags after filtering in treatment: 2422564 INFO @ Sun, 21 Jun 2020 20:02:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:02:57: #1 finished! INFO @ Sun, 21 Jun 2020 20:02:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:02:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:02:57: #2 number of paired peaks: 737 WARNING @ Sun, 21 Jun 2020 20:02:57: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Sun, 21 Jun 2020 20:02:57: start model_add_line... INFO @ Sun, 21 Jun 2020 20:02:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:02:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:02:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:02:57: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 20:02:57: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 20:02:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.10_model.r WARNING @ Sun, 21 Jun 2020 20:02:57: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:02:57: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 21 Jun 2020 20:02:57: #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 20:02:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:02:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:03:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:03:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:03:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:03:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.10_summits.bed INFO @ Sun, 21 Jun 2020 20:03:06: Done! pass1 - making usageList (394 chroms): 1 millis pass2 - checking and writing primary data (683 records, 4 fields): 11 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 @ Sun, 21 Jun 2020 20:03:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.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 20:03:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:03:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:03:16: 1000000 INFO @ Sun, 21 Jun 2020 20:03:23: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:03:26: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:03:26: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:03:26: #1 total tags in treatment: 2422597 INFO @ Sun, 21 Jun 2020 20:03:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:03:26: #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 20:03:26: #1 tags after filtering in treatment: 2422564 INFO @ Sun, 21 Jun 2020 20:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:03:26: #1 finished! INFO @ Sun, 21 Jun 2020 20:03:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:03:27: #2 number of paired peaks: 737 WARNING @ Sun, 21 Jun 2020 20:03:27: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Sun, 21 Jun 2020 20:03:27: start model_add_line... INFO @ Sun, 21 Jun 2020 20:03:27: start X-correlation... INFO @ Sun, 21 Jun 2020 20:03:27: end of X-cor INFO @ Sun, 21 Jun 2020 20:03:27: #2 finished! INFO @ Sun, 21 Jun 2020 20:03:27: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 20:03:27: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 20:03:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.20_model.r WARNING @ Sun, 21 Jun 2020 20:03:27: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:03:27: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 21 Jun 2020 20:03:27: #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 20:03:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:03:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:03:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:03:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:03:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:03:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937194/SRX3937194.20_summits.bed INFO @ Sun, 21 Jun 2020 20:03:36: Done! pass1 - making usageList (207 chroms): 1 millis pass2 - checking and writing primary data (291 records, 4 fields): 8 millis CompletedMACS2peakCalling