Job ID = 6455723 SRX = SRX288020 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:16:06 prefetch.2.10.7: 1) Downloading 'SRR870209'... 2020-06-21T10:16:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:48 prefetch.2.10.7: 1) 'SRR870209' was downloaded successfully Read 21425213 spots for SRR870209/SRR870209.sra Written 21425213 spots for SRR870209/SRR870209.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: 00:08:38 21425213 reads; of these: 21425213 (100.00%) were unpaired; of these: 5522132 (25.77%) aligned 0 times 5814739 (27.14%) aligned exactly 1 time 10088342 (47.09%) aligned >1 times 74.23% overall alignment rate Time searching: 00:08:38 Overall time: 00:08:38 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] 9157802 / 15903081 = 0.5759 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 19:34:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.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 19:34:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:07: 1000000 INFO @ Sun, 21 Jun 2020 19:34:14: 2000000 INFO @ Sun, 21 Jun 2020 19:34:22: 3000000 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 19:34:29: 4000000 INFO @ Sun, 21 Jun 2020 19:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.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 19:34:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:37: 5000000 INFO @ Sun, 21 Jun 2020 19:34:38: 1000000 INFO @ Sun, 21 Jun 2020 19:34:46: 2000000 INFO @ Sun, 21 Jun 2020 19:34:46: 6000000 INFO @ Sun, 21 Jun 2020 19:34:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:53: #1 total tags in treatment: 6745279 INFO @ Sun, 21 Jun 2020 19:34:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:53: #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 19:34:53: #1 tags after filtering in treatment: 6745276 INFO @ Sun, 21 Jun 2020 19:34:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:54: #2 number of paired peaks: 1535 INFO @ Sun, 21 Jun 2020 19:34:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:54: 3000000 INFO @ Sun, 21 Jun 2020 19:34:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:54: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:34:54: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 19:34:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.05_model.r WARNING @ Sun, 21 Jun 2020 19:34:54: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:54: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 19:34:54: #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 19:34:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:54: #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 19:35:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.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 19:35:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:01: 4000000 INFO @ Sun, 21 Jun 2020 19:35:08: 5000000 INFO @ Sun, 21 Jun 2020 19:35:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:08: 1000000 INFO @ Sun, 21 Jun 2020 19:35:15: 6000000 INFO @ Sun, 21 Jun 2020 19:35:15: 2000000 INFO @ Sun, 21 Jun 2020 19:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.05_summits.bed INFO @ Sun, 21 Jun 2020 19:35:15: Done! pass1 - making usageList (753 chroms): 1 millis pass2 - checking and writing primary data (3033 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:21: #1 total tags in treatment: 6745279 INFO @ Sun, 21 Jun 2020 19:35:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:21: #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 19:35:21: #1 tags after filtering in treatment: 6745276 INFO @ Sun, 21 Jun 2020 19:35:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:22: #2 number of paired peaks: 1535 INFO @ Sun, 21 Jun 2020 19:35:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:22: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:35:22: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 19:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.10_model.r WARNING @ Sun, 21 Jun 2020 19:35:22: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:22: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 19:35:22: #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 19:35:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:22: 3000000 INFO @ Sun, 21 Jun 2020 19:35:29: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:35:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:36: 5000000 INFO @ Sun, 21 Jun 2020 19:35:42: 6000000 INFO @ Sun, 21 Jun 2020 19:35:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.10_summits.bed INFO @ Sun, 21 Jun 2020 19:35:43: Done! pass1 - making usageList (588 chroms): 2 millis pass2 - checking and writing primary data (2178 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:35:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:47: #1 total tags in treatment: 6745279 INFO @ Sun, 21 Jun 2020 19:35:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:47: #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 19:35:48: #1 tags after filtering in treatment: 6745276 INFO @ Sun, 21 Jun 2020 19:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:48: #2 number of paired peaks: 1535 INFO @ Sun, 21 Jun 2020 19:35:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:48: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:35:48: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 19:35:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.20_model.r WARNING @ Sun, 21 Jun 2020 19:35:48: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:48: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 19:35:48: #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 19:35:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288020/SRX288020.20_summits.bed INFO @ Sun, 21 Jun 2020 19:36:09: Done! pass1 - making usageList (461 chroms): 1 millis pass2 - checking and writing primary data (1374 records, 4 fields): 14 millis CompletedMACS2peakCalling