Job ID = 6455679 SRX = SRX287983 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:18:36 prefetch.2.10.7: 1) Downloading 'SRR870172'... 2020-06-21T10:18:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:21 prefetch.2.10.7: 'SRR870172' is valid 2020-06-21T10:21:21 prefetch.2.10.7: 1) 'SRR870172' was downloaded successfully Read 13809114 spots for SRR870172/SRR870172.sra Written 13809114 spots for SRR870172/SRR870172.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: 00:04:09 13809114 reads; of these: 13809114 (100.00%) were unpaired; of these: 756586 (5.48%) aligned 0 times 9039900 (65.46%) aligned exactly 1 time 4012628 (29.06%) aligned >1 times 94.52% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 2217204 / 13052528 = 0.1699 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 19:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.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 19:29:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:44: 1000000 INFO @ Sun, 21 Jun 2020 19:29:50: 2000000 INFO @ Sun, 21 Jun 2020 19:29:55: 3000000 INFO @ Sun, 21 Jun 2020 19:30:01: 4000000 INFO @ Sun, 21 Jun 2020 19:30:06: 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 @ Sun, 21 Jun 2020 19:30:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.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 19:30:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:12: 6000000 INFO @ Sun, 21 Jun 2020 19:30:15: 1000000 INFO @ Sun, 21 Jun 2020 19:30:18: 7000000 INFO @ Sun, 21 Jun 2020 19:30:21: 2000000 INFO @ Sun, 21 Jun 2020 19:30:24: 8000000 INFO @ Sun, 21 Jun 2020 19:30:27: 3000000 INFO @ Sun, 21 Jun 2020 19:30:31: 9000000 INFO @ Sun, 21 Jun 2020 19:30:33: 4000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 19:30:37: 10000000 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 19:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.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 19:30:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:39: 5000000 INFO @ Sun, 21 Jun 2020 19:30:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:42: #1 total tags in treatment: 10835324 INFO @ Sun, 21 Jun 2020 19:30:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:42: #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 19:30:43: #1 tags after filtering in treatment: 10835324 INFO @ Sun, 21 Jun 2020 19:30:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:43: #2 number of paired peaks: 731 WARNING @ Sun, 21 Jun 2020 19:30:43: Fewer paired peaks (731) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 731 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:43: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:44: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:30:44: #2 alternative fragment length(s) may be 4,44,540 bps INFO @ Sun, 21 Jun 2020 19:30:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.05_model.r WARNING @ Sun, 21 Jun 2020 19:30:44: #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 19:30:44: #2 You may need to consider one of the other alternative d(s): 4,44,540 WARNING @ Sun, 21 Jun 2020 19:30:44: #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 19:30:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:45: 1000000 INFO @ Sun, 21 Jun 2020 19:30:45: 6000000 INFO @ Sun, 21 Jun 2020 19:30:51: 2000000 INFO @ Sun, 21 Jun 2020 19:30:51: 7000000 INFO @ Sun, 21 Jun 2020 19:30:57: 3000000 INFO @ Sun, 21 Jun 2020 19:30:57: 8000000 INFO @ Sun, 21 Jun 2020 19:31:03: 4000000 INFO @ Sun, 21 Jun 2020 19:31:04: 9000000 INFO @ Sun, 21 Jun 2020 19:31:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:09: 5000000 INFO @ Sun, 21 Jun 2020 19:31:10: 10000000 INFO @ Sun, 21 Jun 2020 19:31:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:15: #1 total tags in treatment: 10835324 INFO @ Sun, 21 Jun 2020 19:31:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:15: #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 19:31:15: 6000000 INFO @ Sun, 21 Jun 2020 19:31:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.05_summits.bed INFO @ Sun, 21 Jun 2020 19:31:15: Done! INFO @ Sun, 21 Jun 2020 19:31:16: #1 tags after filtering in treatment: 10835324 INFO @ Sun, 21 Jun 2020 19:31:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:16: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (571 chroms): 1 millis pass2 - checking and writing primary data (2221 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:16: #2 number of paired peaks: 731 WARNING @ Sun, 21 Jun 2020 19:31:16: Fewer paired peaks (731) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 731 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:16: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:31:16: #2 alternative fragment length(s) may be 4,44,540 bps INFO @ Sun, 21 Jun 2020 19:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.10_model.r WARNING @ Sun, 21 Jun 2020 19:31:16: #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 19:31:16: #2 You may need to consider one of the other alternative d(s): 4,44,540 WARNING @ Sun, 21 Jun 2020 19:31:16: #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 19:31:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:21: 7000000 INFO @ Sun, 21 Jun 2020 19:31:27: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:31:33: 9000000 INFO @ Sun, 21 Jun 2020 19:31:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:38: 10000000 INFO @ Sun, 21 Jun 2020 19:31:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:43: #1 total tags in treatment: 10835324 INFO @ Sun, 21 Jun 2020 19:31:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:43: #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 19:31:44: #1 tags after filtering in treatment: 10835324 INFO @ Sun, 21 Jun 2020 19:31:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:44: #2 number of paired peaks: 731 WARNING @ Sun, 21 Jun 2020 19:31:44: Fewer paired peaks (731) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 731 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:45: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:31:45: #2 alternative fragment length(s) may be 4,44,540 bps INFO @ Sun, 21 Jun 2020 19:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.20_model.r WARNING @ Sun, 21 Jun 2020 19:31:45: #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 19:31:45: #2 You may need to consider one of the other alternative d(s): 4,44,540 WARNING @ Sun, 21 Jun 2020 19:31:45: #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 19:31:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.10_summits.bed INFO @ Sun, 21 Jun 2020 19:31:48: Done! pass1 - making usageList (487 chroms): 1 millis pass2 - checking and writing primary data (1793 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:32:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287983/SRX287983.20_summits.bed INFO @ Sun, 21 Jun 2020 19:32:16: Done! pass1 - making usageList (318 chroms): 1 millis pass2 - checking and writing primary data (692 records, 4 fields): 9 millis CompletedMACS2peakCalling