Job ID = 6453956 SRX = SRX170984 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:49:34 prefetch.2.10.7: 1) Downloading 'SRR527323'... 2020-06-21T08:49:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:06:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:06:15 prefetch.2.10.7: 1) 'SRR527323' was downloaded successfully Read 56762933 spots for SRR527323/SRR527323.sra Written 56762933 spots for SRR527323/SRR527323.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: 00:08:15 56762933 reads; of these: 56762933 (100.00%) were unpaired; of these: 37007171 (65.20%) aligned 0 times 14456521 (25.47%) aligned exactly 1 time 5299241 (9.34%) aligned >1 times 34.80% overall alignment rate Time searching: 00:08:15 Overall time: 00:08:15 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 12 files... [bam_rmdupse_core] 12234331 / 19755762 = 0.6193 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 18:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.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 18:21:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:52: 1000000 INFO @ Sun, 21 Jun 2020 18:21:57: 2000000 INFO @ Sun, 21 Jun 2020 18:22:02: 3000000 INFO @ Sun, 21 Jun 2020 18:22:07: 4000000 INFO @ Sun, 21 Jun 2020 18:22:12: 5000000 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 18:22:17: 6000000 INFO @ Sun, 21 Jun 2020 18:22:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.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 18:22:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:22: 7000000 INFO @ Sun, 21 Jun 2020 18:22:22: 1000000 INFO @ Sun, 21 Jun 2020 18:22:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:22:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:22:25: #1 total tags in treatment: 7521431 INFO @ Sun, 21 Jun 2020 18:22:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:25: #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 18:22:25: #1 tags after filtering in treatment: 7521349 INFO @ Sun, 21 Jun 2020 18:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:26: #2 number of paired peaks: 2971 INFO @ Sun, 21 Jun 2020 18:22:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:26: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 18:22:26: #2 alternative fragment length(s) may be 4,70 bps INFO @ Sun, 21 Jun 2020 18:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.05_model.r WARNING @ Sun, 21 Jun 2020 18:22:26: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:26: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Sun, 21 Jun 2020 18:22:26: #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 18:22:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:27: 2000000 INFO @ Sun, 21 Jun 2020 18:22:32: 3000000 INFO @ Sun, 21 Jun 2020 18:22:37: 4000000 INFO @ Sun, 21 Jun 2020 18:22:42: 5000000 INFO @ Sun, 21 Jun 2020 18:22:43: #3 Call peaks for each chromosome... 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 18:22:47: 6000000 INFO @ Sun, 21 Jun 2020 18:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.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 18:22:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.05_summits.bed INFO @ Sun, 21 Jun 2020 18:22:51: Done! INFO @ Sun, 21 Jun 2020 18:22:52: 7000000 INFO @ Sun, 21 Jun 2020 18:22:53: 1000000 pass1 - making usageList (785 chroms): 2 millis pass2 - checking and writing primary data (5487 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:22:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:22:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:22:55: #1 total tags in treatment: 7521431 INFO @ Sun, 21 Jun 2020 18:22:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:55: #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 18:22:56: #1 tags after filtering in treatment: 7521349 INFO @ Sun, 21 Jun 2020 18:22:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:56: #2 number of paired peaks: 2971 INFO @ Sun, 21 Jun 2020 18:22:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:57: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 18:22:57: #2 alternative fragment length(s) may be 4,70 bps INFO @ Sun, 21 Jun 2020 18:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.10_model.r WARNING @ Sun, 21 Jun 2020 18:22:57: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:57: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Sun, 21 Jun 2020 18:22:57: #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 18:22:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:58: 2000000 INFO @ Sun, 21 Jun 2020 18:23:03: 3000000 INFO @ Sun, 21 Jun 2020 18:23:08: 4000000 INFO @ Sun, 21 Jun 2020 18:23:13: 5000000 INFO @ Sun, 21 Jun 2020 18:23:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:18: 6000000 INFO @ Sun, 21 Jun 2020 18:23:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.10_summits.bed INFO @ Sun, 21 Jun 2020 18:23:21: Done! pass1 - making usageList (576 chroms): 1 millis pass2 - checking and writing primary data (3032 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:23:23: 7000000 INFO @ Sun, 21 Jun 2020 18:23:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:23:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:23:25: #1 total tags in treatment: 7521431 INFO @ Sun, 21 Jun 2020 18:23:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:25: #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 18:23:26: #1 tags after filtering in treatment: 7521349 INFO @ Sun, 21 Jun 2020 18:23:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:26: #2 number of paired peaks: 2971 INFO @ Sun, 21 Jun 2020 18:23:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:27: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 18:23:27: #2 alternative fragment length(s) may be 4,70 bps INFO @ Sun, 21 Jun 2020 18:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.20_model.r WARNING @ Sun, 21 Jun 2020 18:23:27: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:23:27: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Sun, 21 Jun 2020 18:23:27: #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 18:23:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:23:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:23:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX170984/SRX170984.20_summits.bed INFO @ Sun, 21 Jun 2020 18:23:51: Done! pass1 - making usageList (351 chroms): 1 millis pass2 - checking and writing primary data (1221 records, 4 fields): 11 millis CompletedMACS2peakCalling