Job ID = 6456498 SRX = SRX3511946 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:48:50 prefetch.2.10.7: 1) Downloading 'SRR6418931'... 2020-06-21T10:48:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:50:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:50:49 prefetch.2.10.7: 1) 'SRR6418931' was downloaded successfully 2020-06-21T10:50:49 prefetch.2.10.7: 'SRR6418931' has 0 unresolved dependencies Read 12207576 spots for SRR6418931/SRR6418931.sra Written 12207576 spots for SRR6418931/SRR6418931.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: 00:04:43 12207576 reads; of these: 12207576 (100.00%) were unpaired; of these: 2814265 (23.05%) aligned 0 times 7603520 (62.29%) aligned exactly 1 time 1789791 (14.66%) aligned >1 times 76.95% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 794790 / 9393311 = 0.0846 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 20:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.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 20:01:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:01:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:01:29: 1000000 INFO @ Sun, 21 Jun 2020 20:01:35: 2000000 INFO @ Sun, 21 Jun 2020 20:01:41: 3000000 INFO @ Sun, 21 Jun 2020 20:01:47: 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 20:01:53: 5000000 INFO @ Sun, 21 Jun 2020 20:01:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.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 20:01:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:01:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:01:59: 6000000 INFO @ Sun, 21 Jun 2020 20:02:01: 1000000 INFO @ Sun, 21 Jun 2020 20:02:06: 7000000 INFO @ Sun, 21 Jun 2020 20:02:08: 2000000 INFO @ Sun, 21 Jun 2020 20:02:12: 8000000 INFO @ Sun, 21 Jun 2020 20:02:16: 3000000 INFO @ Sun, 21 Jun 2020 20:02:16: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:02:16: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:02:16: #1 total tags in treatment: 8598521 INFO @ Sun, 21 Jun 2020 20:02:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:02:16: #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 20:02:17: #1 tags after filtering in treatment: 8598498 INFO @ Sun, 21 Jun 2020 20:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:02:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:02:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:02:18: #2 number of paired peaks: 2255 INFO @ Sun, 21 Jun 2020 20:02:18: start model_add_line... INFO @ Sun, 21 Jun 2020 20:02:18: start X-correlation... INFO @ Sun, 21 Jun 2020 20:02:18: end of X-cor INFO @ Sun, 21 Jun 2020 20:02:18: #2 finished! INFO @ Sun, 21 Jun 2020 20:02:18: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 20:02:18: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sun, 21 Jun 2020 20:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.05_model.r WARNING @ Sun, 21 Jun 2020 20:02:18: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:02:18: #2 You may need to consider one of the other alternative d(s): 4,175 WARNING @ Sun, 21 Jun 2020 20:02:18: #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 20:02:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:02:18: #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 20:02:23: 4000000 INFO @ Sun, 21 Jun 2020 20:02:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.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 20:02:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:02:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:02:31: 5000000 INFO @ Sun, 21 Jun 2020 20:02:32: 1000000 INFO @ Sun, 21 Jun 2020 20:02:38: 6000000 INFO @ Sun, 21 Jun 2020 20:02:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:02:40: 2000000 INFO @ Sun, 21 Jun 2020 20:02:45: 7000000 INFO @ Sun, 21 Jun 2020 20:02:47: 3000000 INFO @ Sun, 21 Jun 2020 20:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:02:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.05_summits.bed INFO @ Sun, 21 Jun 2020 20:02:48: Done! pass1 - making usageList (538 chroms): 1 millis pass2 - checking and writing primary data (1714 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:02:53: 8000000 INFO @ Sun, 21 Jun 2020 20:02:55: 4000000 INFO @ Sun, 21 Jun 2020 20:02:58: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:02:58: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:02:58: #1 total tags in treatment: 8598521 INFO @ Sun, 21 Jun 2020 20:02:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:02:58: #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 20:02:58: #1 tags after filtering in treatment: 8598498 INFO @ Sun, 21 Jun 2020 20:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:02:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:02:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:02:59: #2 number of paired peaks: 2255 INFO @ Sun, 21 Jun 2020 20:02:59: start model_add_line... INFO @ Sun, 21 Jun 2020 20:02:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:02:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:02:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:02:59: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 20:02:59: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sun, 21 Jun 2020 20:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.10_model.r WARNING @ Sun, 21 Jun 2020 20:02:59: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:02:59: #2 You may need to consider one of the other alternative d(s): 4,175 WARNING @ Sun, 21 Jun 2020 20:02:59: #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 20:02:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:03:02: 5000000 INFO @ Sun, 21 Jun 2020 20:03:09: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:03:16: 7000000 INFO @ Sun, 21 Jun 2020 20:03:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:03:23: 8000000 INFO @ Sun, 21 Jun 2020 20:03:27: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:03:27: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:03:27: #1 total tags in treatment: 8598521 INFO @ Sun, 21 Jun 2020 20:03:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:03:27: #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 20:03:28: #1 tags after filtering in treatment: 8598498 INFO @ Sun, 21 Jun 2020 20:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:03:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:03:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:03:28: #2 number of paired peaks: 2255 INFO @ Sun, 21 Jun 2020 20:03:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:03:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:03:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:03:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.10_summits.bed INFO @ Sun, 21 Jun 2020 20:03:28: Done! INFO @ Sun, 21 Jun 2020 20:03:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:03:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:03:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:03:28: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 20:03:28: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sun, 21 Jun 2020 20:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.20_model.r WARNING @ Sun, 21 Jun 2020 20:03:28: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:03:28: #2 You may need to consider one of the other alternative d(s): 4,175 WARNING @ Sun, 21 Jun 2020 20:03:28: #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 20:03:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:03:28: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (377 chroms): 1 millis pass2 - checking and writing primary data (812 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:03:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:03:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:03:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:03:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511946/SRX3511946.20_summits.bed INFO @ Sun, 21 Jun 2020 20:03:57: Done! pass1 - making usageList (195 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 6 millis CompletedMACS2peakCalling