Job ID = 6455087 SRX = SRX2663651 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:40:25 prefetch.2.10.7: 1) Downloading 'SRR5368387'... 2020-06-21T09:40:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:43:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:43:20 prefetch.2.10.7: 1) 'SRR5368387' was downloaded successfully 2020-06-21T09:43:20 prefetch.2.10.7: 'SRR5368387' has 0 unresolved dependencies Read 17851978 spots for SRR5368387/SRR5368387.sra Written 17851978 spots for SRR5368387/SRR5368387.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: 00:03:45 17851978 reads; of these: 17851978 (100.00%) were unpaired; of these: 8614338 (48.25%) aligned 0 times 6391507 (35.80%) aligned exactly 1 time 2846133 (15.94%) aligned >1 times 51.75% overall alignment rate Time searching: 00:03:45 Overall time: 00:03:45 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] 6890567 / 9237640 = 0.7459 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 18:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.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 18:50:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:55: 1000000 INFO @ Sun, 21 Jun 2020 18:51:03: 2000000 INFO @ Sun, 21 Jun 2020 18:51:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:51:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:51:05: #1 total tags in treatment: 2347073 INFO @ Sun, 21 Jun 2020 18:51:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:05: #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 18:51:06: #1 tags after filtering in treatment: 2347051 INFO @ Sun, 21 Jun 2020 18:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:06: #2 number of paired peaks: 1455 INFO @ Sun, 21 Jun 2020 18:51:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:06: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 18:51:06: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 21 Jun 2020 18:51:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.05_model.r WARNING @ Sun, 21 Jun 2020 18:51:06: #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 18:51:06: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 21 Jun 2020 18:51:06: #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 18:51:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.05_summits.bed INFO @ Sun, 21 Jun 2020 18:51:14: Done! pass1 - making usageList (531 chroms): 2 millis pass2 - checking and writing primary data (1863 records, 4 fields): 31 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 @ Sun, 21 Jun 2020 18:51:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.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 18:51:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:26: 1000000 INFO @ Sun, 21 Jun 2020 18:51:34: 2000000 INFO @ Sun, 21 Jun 2020 18:51:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:51:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:51:36: #1 total tags in treatment: 2347073 INFO @ Sun, 21 Jun 2020 18:51:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:36: #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 18:51:37: #1 tags after filtering in treatment: 2347051 INFO @ Sun, 21 Jun 2020 18:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:37: #2 number of paired peaks: 1455 INFO @ Sun, 21 Jun 2020 18:51:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:37: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 18:51:37: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 21 Jun 2020 18:51:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.10_model.r WARNING @ Sun, 21 Jun 2020 18:51:37: #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 18:51:37: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 21 Jun 2020 18:51:37: #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 18:51:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.10_summits.bed INFO @ Sun, 21 Jun 2020 18:51:45: Done! pass1 - making usageList (377 chroms): 1 millis pass2 - checking and writing primary data (883 records, 4 fields): 22 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 @ Sun, 21 Jun 2020 18:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.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 18:51:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:56: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:03: 2000000 INFO @ Sun, 21 Jun 2020 18:52:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:52:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:52:06: #1 total tags in treatment: 2347073 INFO @ Sun, 21 Jun 2020 18:52:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:06: #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 18:52:06: #1 tags after filtering in treatment: 2347051 INFO @ Sun, 21 Jun 2020 18:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:07: #2 number of paired peaks: 1455 INFO @ Sun, 21 Jun 2020 18:52:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:07: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 18:52:07: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 21 Jun 2020 18:52:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.20_model.r WARNING @ Sun, 21 Jun 2020 18:52:07: #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 18:52:07: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 21 Jun 2020 18:52:07: #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 18:52:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:52:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2663651/SRX2663651.20_summits.bed INFO @ Sun, 21 Jun 2020 18:52:15: Done! pass1 - making usageList (156 chroms): 1 millis pass2 - checking and writing primary data (332 records, 4 fields): 10 millis CompletedMACS2peakCalling