Job ID = 6455294 SRX = SRX287671 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:58:10 prefetch.2.10.7: 1) Downloading 'SRR869859'... 2020-06-21T09:58:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:00:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:00:08 prefetch.2.10.7: 'SRR869859' is valid 2020-06-21T10:00:08 prefetch.2.10.7: 1) 'SRR869859' was downloaded successfully Read 14400973 spots for SRR869859/SRR869859.sra Written 14400973 spots for SRR869859/SRR869859.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: 00:07:53 14400973 reads; of these: 14400973 (100.00%) were unpaired; of these: 1300186 (9.03%) aligned 0 times 2409121 (16.73%) aligned exactly 1 time 10691666 (74.24%) aligned >1 times 90.97% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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] 6704298 / 13100787 = 0.5117 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 19:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.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 19:11:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:59: 1000000 INFO @ Sun, 21 Jun 2020 19:12:05: 2000000 INFO @ Sun, 21 Jun 2020 19:12:12: 3000000 INFO @ Sun, 21 Jun 2020 19:12:19: 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 19:12:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.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 19:12:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:26: 5000000 INFO @ Sun, 21 Jun 2020 19:12:30: 1000000 INFO @ Sun, 21 Jun 2020 19:12:34: 6000000 INFO @ Sun, 21 Jun 2020 19:12:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:37: #1 total tags in treatment: 6396489 INFO @ Sun, 21 Jun 2020 19:12:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:37: #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 19:12:38: 2000000 INFO @ Sun, 21 Jun 2020 19:12:38: #1 tags after filtering in treatment: 6396486 INFO @ Sun, 21 Jun 2020 19:12:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:39: #2 number of paired peaks: 6194 INFO @ Sun, 21 Jun 2020 19:12:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:39: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 19:12:39: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sun, 21 Jun 2020 19:12:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.05_model.r WARNING @ Sun, 21 Jun 2020 19:12:39: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:39: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sun, 21 Jun 2020 19:12:39: #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 19:12:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:45: 3000000 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 19:12:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:52: 4000000 INFO @ Sun, 21 Jun 2020 19:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.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 19:12:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.05_summits.bed INFO @ Sun, 21 Jun 2020 19:12:58: Done! pass1 - making usageList (1258 chroms): 2 millis pass2 - checking and writing primary data (5082 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:00: 5000000 INFO @ Sun, 21 Jun 2020 19:13:00: 1000000 INFO @ Sun, 21 Jun 2020 19:13:08: 6000000 INFO @ Sun, 21 Jun 2020 19:13:08: 2000000 INFO @ Sun, 21 Jun 2020 19:13:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:11: #1 total tags in treatment: 6396489 INFO @ Sun, 21 Jun 2020 19:13:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:11: #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 19:13:11: #1 tags after filtering in treatment: 6396486 INFO @ Sun, 21 Jun 2020 19:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:12: #2 number of paired peaks: 6194 INFO @ Sun, 21 Jun 2020 19:13:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:12: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 19:13:12: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sun, 21 Jun 2020 19:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.10_model.r WARNING @ Sun, 21 Jun 2020 19:13:12: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:12: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sun, 21 Jun 2020 19:13:12: #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 19:13:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:15: 3000000 INFO @ Sun, 21 Jun 2020 19:13:21: 4000000 INFO @ Sun, 21 Jun 2020 19:13:24: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:13:28: 5000000 INFO @ Sun, 21 Jun 2020 19:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.10_summits.bed INFO @ Sun, 21 Jun 2020 19:13:30: Done! pass1 - making usageList (1003 chroms): 2 millis pass2 - checking and writing primary data (3433 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:35: 6000000 INFO @ Sun, 21 Jun 2020 19:13:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:38: #1 total tags in treatment: 6396489 INFO @ Sun, 21 Jun 2020 19:13:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:13:38: #1 tags after filtering in treatment: 6396486 INFO @ Sun, 21 Jun 2020 19:13:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:39: #2 number of paired peaks: 6194 INFO @ Sun, 21 Jun 2020 19:13:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:39: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 19:13:39: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sun, 21 Jun 2020 19:13:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.20_model.r WARNING @ Sun, 21 Jun 2020 19:13:39: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:39: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sun, 21 Jun 2020 19:13:39: #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 19:13:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287671/SRX287671.20_summits.bed INFO @ Sun, 21 Jun 2020 19:14:00: Done! pass1 - making usageList (690 chroms): 1 millis pass2 - checking and writing primary data (1892 records, 4 fields): 30 millis CompletedMACS2peakCalling