Job ID = 6452992 SRX = SRX085410 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:55:15 prefetch.2.10.7: 1) Downloading 'SRR317188'... 2020-06-21T07:55:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:57:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:57:15 prefetch.2.10.7: 1) 'SRR317188' was downloaded successfully Read 21810536 spots for SRR317188/SRR317188.sra Written 21810536 spots for SRR317188/SRR317188.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: 00:06:33 21810536 reads; of these: 21810536 (100.00%) were unpaired; of these: 6273992 (28.77%) aligned 0 times 10894060 (49.95%) aligned exactly 1 time 4642484 (21.29%) aligned >1 times 71.23% overall alignment rate Time searching: 00:06:33 Overall time: 00:06:33 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] 4689220 / 15536544 = 0.3018 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 17:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.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 17:08:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:50: 1000000 INFO @ Sun, 21 Jun 2020 17:08:55: 2000000 INFO @ Sun, 21 Jun 2020 17:09:00: 3000000 INFO @ Sun, 21 Jun 2020 17:09:05: 4000000 INFO @ Sun, 21 Jun 2020 17:09:10: 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 17:09:15: 6000000 INFO @ Sun, 21 Jun 2020 17:09:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.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 17:09:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:09:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:09:20: 7000000 INFO @ Sun, 21 Jun 2020 17:09:21: 1000000 INFO @ Sun, 21 Jun 2020 17:09:25: 8000000 INFO @ Sun, 21 Jun 2020 17:09:26: 2000000 INFO @ Sun, 21 Jun 2020 17:09:30: 9000000 INFO @ Sun, 21 Jun 2020 17:09:30: 3000000 INFO @ Sun, 21 Jun 2020 17:09:35: 10000000 INFO @ Sun, 21 Jun 2020 17:09:35: 4000000 INFO @ Sun, 21 Jun 2020 17:09:39: #1 tag size is determined as 54 bps INFO @ Sun, 21 Jun 2020 17:09:39: #1 tag size = 54 INFO @ Sun, 21 Jun 2020 17:09:39: #1 total tags in treatment: 10847324 INFO @ Sun, 21 Jun 2020 17:09:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:39: #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 17:09:39: #1 tags after filtering in treatment: 10847246 INFO @ Sun, 21 Jun 2020 17:09:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:40: #2 number of paired peaks: 1114 INFO @ Sun, 21 Jun 2020 17:09:40: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:40: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:40: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:40: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:40: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 17:09:40: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 17:09:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.05_model.r WARNING @ Sun, 21 Jun 2020 17:09:40: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:09:40: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 17:09:40: #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 17:09:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:40: 5000000 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 17:09:45: 6000000 INFO @ Sun, 21 Jun 2020 17:09:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.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 17:09:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:09:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:09:50: 7000000 INFO @ Sun, 21 Jun 2020 17:09:51: 1000000 INFO @ Sun, 21 Jun 2020 17:09:55: 8000000 INFO @ Sun, 21 Jun 2020 17:09:56: 2000000 INFO @ Sun, 21 Jun 2020 17:10:00: 9000000 INFO @ Sun, 21 Jun 2020 17:10:01: 3000000 INFO @ Sun, 21 Jun 2020 17:10:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:05: 10000000 INFO @ Sun, 21 Jun 2020 17:10:06: 4000000 INFO @ Sun, 21 Jun 2020 17:10:10: #1 tag size is determined as 54 bps INFO @ Sun, 21 Jun 2020 17:10:10: #1 tag size = 54 INFO @ Sun, 21 Jun 2020 17:10:10: #1 total tags in treatment: 10847324 INFO @ Sun, 21 Jun 2020 17:10:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:10:10: #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 17:10:10: #1 tags after filtering in treatment: 10847246 INFO @ Sun, 21 Jun 2020 17:10:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:10:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:10:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:10:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:10:10: 5000000 INFO @ Sun, 21 Jun 2020 17:10:11: #2 number of paired peaks: 1114 INFO @ Sun, 21 Jun 2020 17:10:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:10:11: start X-correlation... INFO @ Sun, 21 Jun 2020 17:10:11: end of X-cor INFO @ Sun, 21 Jun 2020 17:10:11: #2 finished! INFO @ Sun, 21 Jun 2020 17:10:11: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 17:10:11: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 17:10:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.10_model.r WARNING @ Sun, 21 Jun 2020 17:10:11: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:10:11: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 17:10:11: #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 17:10:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:10:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.05_summits.bed INFO @ Sun, 21 Jun 2020 17:10:12: Done! pass1 - making usageList (683 chroms): 1 millis pass2 - checking and writing primary data (3294 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:10:15: 6000000 INFO @ Sun, 21 Jun 2020 17:10:20: 7000000 INFO @ Sun, 21 Jun 2020 17:10:25: 8000000 INFO @ Sun, 21 Jun 2020 17:10:30: 9000000 INFO @ Sun, 21 Jun 2020 17:10:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:35: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:10:39: #1 tag size is determined as 54 bps INFO @ Sun, 21 Jun 2020 17:10:39: #1 tag size = 54 INFO @ Sun, 21 Jun 2020 17:10:39: #1 total tags in treatment: 10847324 INFO @ Sun, 21 Jun 2020 17:10:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:10:39: #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 17:10:40: #1 tags after filtering in treatment: 10847246 INFO @ Sun, 21 Jun 2020 17:10:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:10:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:10:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:10:41: #2 number of paired peaks: 1114 INFO @ Sun, 21 Jun 2020 17:10:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:10:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:10:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:10:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:10:41: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 17:10:41: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 17:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.20_model.r WARNING @ Sun, 21 Jun 2020 17:10:41: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:10:41: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 17:10:41: #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 17:10:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:10:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.10_summits.bed INFO @ Sun, 21 Jun 2020 17:10:43: Done! pass1 - making usageList (517 chroms): 1 millis pass2 - checking and writing primary data (1795 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:11:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:11:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:11:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:11:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085410/SRX085410.20_summits.bed INFO @ Sun, 21 Jun 2020 17:11:13: Done! pass1 - making usageList (296 chroms): 0 millis pass2 - checking and writing primary data (697 records, 4 fields): 9 millis CompletedMACS2peakCalling