Job ID = 6458918 SRX = SRX5775923 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:40:26 prefetch.2.10.7: 1) Downloading 'SRR8997126'... 2020-06-21T12:40:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:42:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:42:45 prefetch.2.10.7: 1) 'SRR8997126' was downloaded successfully Read 19842281 spots for SRR8997126/SRR8997126.sra Written 19842281 spots for SRR8997126/SRR8997126.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 19842281 reads; of these: 19842281 (100.00%) were unpaired; of these: 14236692 (71.75%) aligned 0 times 4078046 (20.55%) aligned exactly 1 time 1527543 (7.70%) aligned >1 times 28.25% 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] 1817315 / 5605589 = 0.3242 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 21:49:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.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 21:49:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:28: 1000000 INFO @ Sun, 21 Jun 2020 21:49:35: 2000000 INFO @ Sun, 21 Jun 2020 21:49:41: 3000000 INFO @ Sun, 21 Jun 2020 21:49:46: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:49:46: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:49:46: #1 total tags in treatment: 3788274 INFO @ Sun, 21 Jun 2020 21:49:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:49:46: #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 21:49:47: #1 tags after filtering in treatment: 3788244 INFO @ Sun, 21 Jun 2020 21:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:49:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:49:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:49:47: #2 number of paired peaks: 1106 INFO @ Sun, 21 Jun 2020 21:49:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:49:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:49:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:49:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:49:47: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 21:49:47: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 21:49:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.05_model.r WARNING @ Sun, 21 Jun 2020 21:49:47: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:49:47: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 21:49:47: #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 21:49:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:49:47: #3 Pre-compute pvalue-qvalue table... 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 21:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.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 21:49:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:49:56: 1000000 INFO @ Sun, 21 Jun 2020 21:50:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:50:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.05_summits.bed INFO @ Sun, 21 Jun 2020 21:50:00: Done! pass1 - making usageList (576 chroms): 1 millis pass2 - checking and writing primary data (2369 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:50:02: 2000000 INFO @ Sun, 21 Jun 2020 21:50:09: 3000000 INFO @ Sun, 21 Jun 2020 21:50:14: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:50:14: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:50:14: #1 total tags in treatment: 3788274 INFO @ Sun, 21 Jun 2020 21:50:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:50:14: #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 21:50:14: #1 tags after filtering in treatment: 3788244 INFO @ Sun, 21 Jun 2020 21:50:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:50:14: #1 finished! INFO @ Sun, 21 Jun 2020 21:50:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:50:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:50:15: #2 number of paired peaks: 1106 INFO @ Sun, 21 Jun 2020 21:50:15: start model_add_line... INFO @ Sun, 21 Jun 2020 21:50:15: start X-correlation... INFO @ Sun, 21 Jun 2020 21:50:15: end of X-cor INFO @ Sun, 21 Jun 2020 21:50:15: #2 finished! INFO @ Sun, 21 Jun 2020 21:50:15: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 21:50:15: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 21:50:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.10_model.r WARNING @ Sun, 21 Jun 2020 21:50:15: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:50:15: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 21:50:15: #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 21:50:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:50:15: #3 Pre-compute pvalue-qvalue table... 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 21:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.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 21:50:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:50:27: 1000000 INFO @ Sun, 21 Jun 2020 21:50:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:50:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:50:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.10_summits.bed INFO @ Sun, 21 Jun 2020 21:50:27: Done! pass1 - making usageList (435 chroms): 1 millis pass2 - checking and writing primary data (1187 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:50:33: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:50:39: 3000000 INFO @ Sun, 21 Jun 2020 21:50:44: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:50:44: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:50:44: #1 total tags in treatment: 3788274 INFO @ Sun, 21 Jun 2020 21:50:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:50:44: #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 21:50:44: #1 tags after filtering in treatment: 3788244 INFO @ Sun, 21 Jun 2020 21:50:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:50:44: #1 finished! INFO @ Sun, 21 Jun 2020 21:50:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:50:45: #2 number of paired peaks: 1106 INFO @ Sun, 21 Jun 2020 21:50:45: start model_add_line... INFO @ Sun, 21 Jun 2020 21:50:45: start X-correlation... INFO @ Sun, 21 Jun 2020 21:50:45: end of X-cor INFO @ Sun, 21 Jun 2020 21:50:45: #2 finished! INFO @ Sun, 21 Jun 2020 21:50:45: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 21:50:45: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 21:50:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.20_model.r WARNING @ Sun, 21 Jun 2020 21:50:45: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:50:45: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 21:50:45: #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 21:50:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:50:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:50:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:50:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:50:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:50:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775923/SRX5775923.20_summits.bed INFO @ Sun, 21 Jun 2020 21:50:57: Done! pass1 - making usageList (257 chroms): 1 millis pass2 - checking and writing primary data (437 records, 4 fields): 8 millis CompletedMACS2peakCalling