Job ID = 6509084 SRX = SRX645127 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:17:29 prefetch.2.10.7: 1) Downloading 'SRR1505727'... 2020-06-26T15:17:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:21:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:21:34 prefetch.2.10.7: 1) 'SRR1505727' was downloaded successfully Read 21733577 spots for SRR1505727/SRR1505727.sra Written 21733577 spots for SRR1505727/SRR1505727.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: 00:07:16 21733577 reads; of these: 21733577 (100.00%) were unpaired; of these: 15976064 (73.51%) aligned 0 times 4201635 (19.33%) aligned exactly 1 time 1555878 (7.16%) aligned >1 times 26.49% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 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] 4335191 / 5757513 = 0.7530 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 @ Sat, 27 Jun 2020 00:32:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.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 @ Sat, 27 Jun 2020 00:32:25: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:32:25: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:32:33: 1000000 INFO @ Sat, 27 Jun 2020 00:32:38: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:32:38: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:32:38: #1 total tags in treatment: 1422322 INFO @ Sat, 27 Jun 2020 00:32:38: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:32:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:32:38: #1 tags after filtering in treatment: 1422145 INFO @ Sat, 27 Jun 2020 00:32:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:32:38: #1 finished! INFO @ Sat, 27 Jun 2020 00:32:38: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:32:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:32:38: #2 number of paired peaks: 1995 INFO @ Sat, 27 Jun 2020 00:32:38: start model_add_line... INFO @ Sat, 27 Jun 2020 00:32:38: start X-correlation... INFO @ Sat, 27 Jun 2020 00:32:38: end of X-cor INFO @ Sat, 27 Jun 2020 00:32:38: #2 finished! INFO @ Sat, 27 Jun 2020 00:32:38: #2 predicted fragment length is 101 bps INFO @ Sat, 27 Jun 2020 00:32:38: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 27 Jun 2020 00:32:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.05_model.r WARNING @ Sat, 27 Jun 2020 00:32:38: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:32:38: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sat, 27 Jun 2020 00:32:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:32:38: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:32:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:32:42: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.05_summits.bed INFO @ Sat, 27 Jun 2020 00:32:44: Done! pass1 - making usageList (574 chroms): 1 millis pass2 - checking and writing primary data (1362 records, 4 fields): 20 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 @ Sat, 27 Jun 2020 00:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.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 @ Sat, 27 Jun 2020 00:32:55: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:32:55: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:33:04: 1000000 INFO @ Sat, 27 Jun 2020 00:33:08: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:33:08: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:33:08: #1 total tags in treatment: 1422322 INFO @ Sat, 27 Jun 2020 00:33:08: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:33:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:33:08: #1 tags after filtering in treatment: 1422145 INFO @ Sat, 27 Jun 2020 00:33:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:33:08: #1 finished! INFO @ Sat, 27 Jun 2020 00:33:08: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:33:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:33:08: #2 number of paired peaks: 1995 INFO @ Sat, 27 Jun 2020 00:33:08: start model_add_line... INFO @ Sat, 27 Jun 2020 00:33:08: start X-correlation... INFO @ Sat, 27 Jun 2020 00:33:08: end of X-cor INFO @ Sat, 27 Jun 2020 00:33:08: #2 finished! INFO @ Sat, 27 Jun 2020 00:33:08: #2 predicted fragment length is 101 bps INFO @ Sat, 27 Jun 2020 00:33:08: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 27 Jun 2020 00:33:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.10_model.r WARNING @ Sat, 27 Jun 2020 00:33:08: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:33:08: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sat, 27 Jun 2020 00:33:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:33:08: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:33:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:33:13: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.10_summits.bed INFO @ Sat, 27 Jun 2020 00:33:15: Done! pass1 - making usageList (435 chroms): 1 millis pass2 - checking and writing primary data (802 records, 4 fields): 15 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 @ Sat, 27 Jun 2020 00:33:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.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 @ Sat, 27 Jun 2020 00:33:25: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:33:25: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:33:34: 1000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:33:38: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:33:38: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:33:38: #1 total tags in treatment: 1422322 INFO @ Sat, 27 Jun 2020 00:33:38: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:33:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:33:39: #1 tags after filtering in treatment: 1422145 INFO @ Sat, 27 Jun 2020 00:33:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:33:39: #1 finished! INFO @ Sat, 27 Jun 2020 00:33:39: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:33:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:33:39: #2 number of paired peaks: 1995 INFO @ Sat, 27 Jun 2020 00:33:39: start model_add_line... INFO @ Sat, 27 Jun 2020 00:33:39: start X-correlation... INFO @ Sat, 27 Jun 2020 00:33:39: end of X-cor INFO @ Sat, 27 Jun 2020 00:33:39: #2 finished! INFO @ Sat, 27 Jun 2020 00:33:39: #2 predicted fragment length is 101 bps INFO @ Sat, 27 Jun 2020 00:33:39: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 27 Jun 2020 00:33:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.20_model.r WARNING @ Sat, 27 Jun 2020 00:33:39: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:33:39: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sat, 27 Jun 2020 00:33:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:33:39: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:33:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:33:43: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:33:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:33:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:33:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645127/SRX645127.20_summits.bed INFO @ Sat, 27 Jun 2020 00:33:45: Done! pass1 - making usageList (241 chroms): 0 millis pass2 - checking and writing primary data (336 records, 4 fields): 10 millis CompletedMACS2peakCalling