Job ID = 6454851 SRX = SRX2592443 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:47:10 prefetch.2.10.7: 1) Downloading 'SRR5289720'... 2020-06-21T09:47:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:48:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:48:27 prefetch.2.10.7: 'SRR5289720' is valid 2020-06-21T09:48:27 prefetch.2.10.7: 1) 'SRR5289720' was downloaded successfully Read 8858510 spots for SRR5289720/SRR5289720.sra Written 8858510 spots for SRR5289720/SRR5289720.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: 00:02:04 8858510 reads; of these: 8858510 (100.00%) were unpaired; of these: 2428693 (27.42%) aligned 0 times 4964092 (56.04%) aligned exactly 1 time 1465725 (16.55%) aligned >1 times 72.58% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 705569 / 6429817 = 0.1097 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 18:53:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.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 18:53:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:24: 1000000 INFO @ Sun, 21 Jun 2020 18:53:30: 2000000 INFO @ Sun, 21 Jun 2020 18:53:36: 3000000 INFO @ Sun, 21 Jun 2020 18:53:42: 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 18:53:48: 5000000 INFO @ Sun, 21 Jun 2020 18:53:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.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 18:53:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:53:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:53:53: #1 total tags in treatment: 5724248 INFO @ Sun, 21 Jun 2020 18:53:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:53: #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 18:53:53: #1 tags after filtering in treatment: 5723999 INFO @ Sun, 21 Jun 2020 18:53:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:54: #2 number of paired peaks: 639 WARNING @ Sun, 21 Jun 2020 18:53:54: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sun, 21 Jun 2020 18:53:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:54: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 18:53:54: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 18:53:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.05_model.r WARNING @ Sun, 21 Jun 2020 18:53:54: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:54: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 18:53:54: #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 18:53:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:55: 1000000 INFO @ Sun, 21 Jun 2020 18:54:01: 2000000 INFO @ Sun, 21 Jun 2020 18:54:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:08: 3000000 INFO @ Sun, 21 Jun 2020 18:54:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.05_summits.bed INFO @ Sun, 21 Jun 2020 18:54:13: Done! pass1 - making usageList (335 chroms): 1 millis pass2 - checking and writing primary data (1813 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:54:14: 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 18:54:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.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 18:54:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:20: 5000000 INFO @ Sun, 21 Jun 2020 18:54:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:54:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:54:25: #1 total tags in treatment: 5724248 INFO @ Sun, 21 Jun 2020 18:54:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:25: #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 18:54:25: 1000000 INFO @ Sun, 21 Jun 2020 18:54:26: #1 tags after filtering in treatment: 5723999 INFO @ Sun, 21 Jun 2020 18:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:26: #2 number of paired peaks: 639 WARNING @ Sun, 21 Jun 2020 18:54:26: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:26: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 18:54:26: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 18:54:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.10_model.r WARNING @ Sun, 21 Jun 2020 18:54:26: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:26: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 18:54:26: #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 18:54:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:32: 2000000 INFO @ Sun, 21 Jun 2020 18:54:38: 3000000 INFO @ Sun, 21 Jun 2020 18:54:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:45: 4000000 INFO @ Sun, 21 Jun 2020 18:54:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.10_summits.bed INFO @ Sun, 21 Jun 2020 18:54:46: Done! pass1 - making usageList (233 chroms): 1 millis pass2 - checking and writing primary data (644 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:54:51: 5000000 INFO @ Sun, 21 Jun 2020 18:54:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:54:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:54:56: #1 total tags in treatment: 5724248 INFO @ Sun, 21 Jun 2020 18:54:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:56: #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 18:54:56: #1 tags after filtering in treatment: 5723999 INFO @ Sun, 21 Jun 2020 18:54:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:57: #2 number of paired peaks: 639 WARNING @ Sun, 21 Jun 2020 18:54:57: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:57: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 18:54:57: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 18:54:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.20_model.r WARNING @ Sun, 21 Jun 2020 18:54:57: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:57: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 18:54:57: #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 18:54:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:55:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592443/SRX2592443.20_summits.bed INFO @ Sun, 21 Jun 2020 18:55:18: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 5 millis CompletedMACS2peakCalling