Job ID = 6498748 SRX = SRX750071 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:16:06 prefetch.2.10.7: 1) Downloading 'SRR1638754'... 2020-06-26T00:16:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:19:36 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:19:36 prefetch.2.10.7: 1) 'SRR1638754' was downloaded successfully Read 37029482 spots for SRR1638754/SRR1638754.sra Written 37029482 spots for SRR1638754/SRR1638754.sra 2020-06-26T00:22:04 prefetch.2.10.7: 1) Downloading 'SRR1638755'... 2020-06-26T00:22:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:24:08 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:24:08 prefetch.2.10.7: 1) 'SRR1638755' was downloaded successfully Read 21812756 spots for SRR1638755/SRR1638755.sra Written 21812756 spots for SRR1638755/SRR1638755.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:22:36 58842238 reads; of these: 58842238 (100.00%) were unpaired; of these: 3414248 (5.80%) aligned 0 times 43788384 (74.42%) aligned exactly 1 time 11639606 (19.78%) aligned >1 times 94.20% overall alignment rate Time searching: 00:22:37 Overall time: 00:22:37 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 24 files... [bam_rmdupse_core] 45649081 / 55427990 = 0.8236 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 10:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.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 10:00:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:00:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:00:43: 1000000 INFO @ Fri, 26 Jun 2020 10:00:50: 2000000 INFO @ Fri, 26 Jun 2020 10:00:57: 3000000 INFO @ Fri, 26 Jun 2020 10:01:04: 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 @ Fri, 26 Jun 2020 10:01:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.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 10:01:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:01:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:01:12: 5000000 INFO @ Fri, 26 Jun 2020 10:01:14: 1000000 INFO @ Fri, 26 Jun 2020 10:01:20: 6000000 INFO @ Fri, 26 Jun 2020 10:01:21: 2000000 INFO @ Fri, 26 Jun 2020 10:01:28: 7000000 INFO @ Fri, 26 Jun 2020 10:01:29: 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 10:01:36: 4000000 INFO @ Fri, 26 Jun 2020 10:01:36: 8000000 INFO @ Fri, 26 Jun 2020 10:01:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.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 10:01:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:01:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:01:43: 5000000 INFO @ Fri, 26 Jun 2020 10:01:44: 1000000 INFO @ Fri, 26 Jun 2020 10:01:45: 9000000 INFO @ Fri, 26 Jun 2020 10:01:51: 6000000 INFO @ Fri, 26 Jun 2020 10:01:51: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 10:01:51: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 10:01:51: #1 total tags in treatment: 9778909 INFO @ Fri, 26 Jun 2020 10:01:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:01:51: #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 10:01:51: #1 tags after filtering in treatment: 9778909 INFO @ Fri, 26 Jun 2020 10:01:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:01:51: #1 finished! INFO @ Fri, 26 Jun 2020 10:01:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:01:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:01:52: 2000000 INFO @ Fri, 26 Jun 2020 10:01:53: #2 number of paired peaks: 6061 INFO @ Fri, 26 Jun 2020 10:01:53: start model_add_line... INFO @ Fri, 26 Jun 2020 10:01:53: start X-correlation... INFO @ Fri, 26 Jun 2020 10:01:53: end of X-cor INFO @ Fri, 26 Jun 2020 10:01:53: #2 finished! INFO @ Fri, 26 Jun 2020 10:01:53: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 10:01:53: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 10:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.05_model.r WARNING @ Fri, 26 Jun 2020 10:01:53: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:01:53: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Fri, 26 Jun 2020 10:01:53: #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 10:01:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:01:59: 7000000 INFO @ Fri, 26 Jun 2020 10:02:00: 3000000 INFO @ Fri, 26 Jun 2020 10:02:06: 8000000 INFO @ Fri, 26 Jun 2020 10:02:07: 4000000 INFO @ Fri, 26 Jun 2020 10:02:14: 9000000 INFO @ Fri, 26 Jun 2020 10:02:15: 5000000 INFO @ Fri, 26 Jun 2020 10:02:19: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 10:02:19: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 10:02:19: #1 total tags in treatment: 9778909 INFO @ Fri, 26 Jun 2020 10:02:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:02:19: #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 10:02:20: #1 tags after filtering in treatment: 9778909 INFO @ Fri, 26 Jun 2020 10:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:02:20: #1 finished! INFO @ Fri, 26 Jun 2020 10:02:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:02:21: #2 number of paired peaks: 6061 INFO @ Fri, 26 Jun 2020 10:02:21: start model_add_line... INFO @ Fri, 26 Jun 2020 10:02:21: start X-correlation... INFO @ Fri, 26 Jun 2020 10:02:21: end of X-cor INFO @ Fri, 26 Jun 2020 10:02:21: #2 finished! INFO @ Fri, 26 Jun 2020 10:02:21: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 10:02:21: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 10:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.10_model.r WARNING @ Fri, 26 Jun 2020 10:02:21: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:02:21: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Fri, 26 Jun 2020 10:02:21: #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 10:02:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:02:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:02:22: 6000000 INFO @ Fri, 26 Jun 2020 10:02:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:02:29: 7000000 INFO @ Fri, 26 Jun 2020 10:02:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:02:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:02:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.05_summits.bed INFO @ Fri, 26 Jun 2020 10:02:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9426 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:02:36: 8000000 INFO @ Fri, 26 Jun 2020 10:02:42: 9000000 INFO @ Fri, 26 Jun 2020 10:02:47: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 10:02:47: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 10:02:47: #1 total tags in treatment: 9778909 INFO @ Fri, 26 Jun 2020 10:02:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:02:47: #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 10:02:47: #1 tags after filtering in treatment: 9778909 INFO @ Fri, 26 Jun 2020 10:02:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:02:47: #1 finished! INFO @ Fri, 26 Jun 2020 10:02:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:02:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:02:49: #2 number of paired peaks: 6061 INFO @ Fri, 26 Jun 2020 10:02:49: start model_add_line... INFO @ Fri, 26 Jun 2020 10:02:49: start X-correlation... INFO @ Fri, 26 Jun 2020 10:02:49: end of X-cor INFO @ Fri, 26 Jun 2020 10:02:49: #2 finished! INFO @ Fri, 26 Jun 2020 10:02:49: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 10:02:49: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 10:02:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.20_model.r WARNING @ Fri, 26 Jun 2020 10:02:49: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:02:49: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Fri, 26 Jun 2020 10:02:49: #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 10:02:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:02:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:02:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.10_summits.bed INFO @ Fri, 26 Jun 2020 10:03:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6531 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:03:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:03:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:03:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:03:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750071/SRX750071.20_summits.bed INFO @ Fri, 26 Jun 2020 10:03:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4374 records, 4 fields): 7 millis CompletedMACS2peakCalling