Job ID = 6498056 SRX = SRX297098 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:57:28 prefetch.2.10.7: 1) Downloading 'SRR886299'... 2020-06-25T22:57:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:00:58 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:00:58 prefetch.2.10.7: 1) 'SRR886299' was downloaded successfully Read 27772748 spots for SRR886299/SRR886299.sra Written 27772748 spots for SRR886299/SRR886299.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: 00:14:17 27772748 reads; of these: 27772748 (100.00%) were unpaired; of these: 6237165 (22.46%) aligned 0 times 8208628 (29.56%) aligned exactly 1 time 13326955 (47.99%) aligned >1 times 77.54% overall alignment rate Time searching: 00:14:17 Overall time: 00:14:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 15540737 / 21535583 = 0.7216 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 @ Fri, 26 Jun 2020 08:21:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.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 @ Fri, 26 Jun 2020 08:21:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:21:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:21:41: 1000000 INFO @ Fri, 26 Jun 2020 08:21:49: 2000000 INFO @ Fri, 26 Jun 2020 08:21:58: 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 @ Fri, 26 Jun 2020 08:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.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 @ Fri, 26 Jun 2020 08:22:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:22:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:22:06: 4000000 INFO @ Fri, 26 Jun 2020 08:22:12: 1000000 INFO @ Fri, 26 Jun 2020 08:22:15: 5000000 INFO @ Fri, 26 Jun 2020 08:22:21: 2000000 INFO @ Fri, 26 Jun 2020 08:22:24: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:22:24: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:22:24: #1 total tags in treatment: 5994846 INFO @ Fri, 26 Jun 2020 08:22:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:22:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:22:24: #1 tags after filtering in treatment: 5994846 INFO @ Fri, 26 Jun 2020 08:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:22:24: #1 finished! INFO @ Fri, 26 Jun 2020 08:22:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:22:25: #2 number of paired peaks: 5164 INFO @ Fri, 26 Jun 2020 08:22:25: start model_add_line... INFO @ Fri, 26 Jun 2020 08:22:25: start X-correlation... INFO @ Fri, 26 Jun 2020 08:22:25: end of X-cor INFO @ Fri, 26 Jun 2020 08:22:25: #2 finished! INFO @ Fri, 26 Jun 2020 08:22:25: #2 predicted fragment length is 73 bps INFO @ Fri, 26 Jun 2020 08:22:25: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 26 Jun 2020 08:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.05_model.r WARNING @ Fri, 26 Jun 2020 08:22:25: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:22:25: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 26 Jun 2020 08:22:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:22:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:22:30: 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 @ Fri, 26 Jun 2020 08:22:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.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 @ Fri, 26 Jun 2020 08:22:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:22:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:22:39: 4000000 INFO @ Fri, 26 Jun 2020 08:22:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:22:42: 1000000 INFO @ Fri, 26 Jun 2020 08:22:48: 5000000 INFO @ Fri, 26 Jun 2020 08:22:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:22:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:22:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.05_summits.bed INFO @ Fri, 26 Jun 2020 08:22:51: Done! INFO @ Fri, 26 Jun 2020 08:22:51: 2000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (14364 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:22:56: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:22:56: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:22:56: #1 total tags in treatment: 5994846 INFO @ Fri, 26 Jun 2020 08:22:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:22:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:22:57: #1 tags after filtering in treatment: 5994846 INFO @ Fri, 26 Jun 2020 08:22:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:22:57: #1 finished! INFO @ Fri, 26 Jun 2020 08:22:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:22:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:22:57: #2 number of paired peaks: 5164 INFO @ Fri, 26 Jun 2020 08:22:57: start model_add_line... INFO @ Fri, 26 Jun 2020 08:22:58: start X-correlation... INFO @ Fri, 26 Jun 2020 08:22:58: end of X-cor INFO @ Fri, 26 Jun 2020 08:22:58: #2 finished! INFO @ Fri, 26 Jun 2020 08:22:58: #2 predicted fragment length is 73 bps INFO @ Fri, 26 Jun 2020 08:22:58: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 26 Jun 2020 08:22:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.10_model.r WARNING @ Fri, 26 Jun 2020 08:22:58: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:22:58: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 26 Jun 2020 08:22:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:22:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:22:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:23:00: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:23:09: 4000000 INFO @ Fri, 26 Jun 2020 08:23:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:23:17: 5000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:23:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:23:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:23:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.10_summits.bed INFO @ Fri, 26 Jun 2020 08:23:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8588 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:23:25: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:23:25: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:23:25: #1 total tags in treatment: 5994846 INFO @ Fri, 26 Jun 2020 08:23:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:23:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:23:25: #1 tags after filtering in treatment: 5994846 INFO @ Fri, 26 Jun 2020 08:23:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:23:25: #1 finished! INFO @ Fri, 26 Jun 2020 08:23:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:23:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:23:26: #2 number of paired peaks: 5164 INFO @ Fri, 26 Jun 2020 08:23:26: start model_add_line... INFO @ Fri, 26 Jun 2020 08:23:26: start X-correlation... INFO @ Fri, 26 Jun 2020 08:23:26: end of X-cor INFO @ Fri, 26 Jun 2020 08:23:26: #2 finished! INFO @ Fri, 26 Jun 2020 08:23:26: #2 predicted fragment length is 73 bps INFO @ Fri, 26 Jun 2020 08:23:26: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 26 Jun 2020 08:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.20_model.r WARNING @ Fri, 26 Jun 2020 08:23:26: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:23:26: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 26 Jun 2020 08:23:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:23:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:23:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:23:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:23:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:23:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX297098/SRX297098.20_summits.bed INFO @ Fri, 26 Jun 2020 08:23:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2974 records, 4 fields): 5 millis CompletedMACS2peakCalling