Job ID = 6458140 SRX = SRX495257 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:12:49 prefetch.2.10.7: 1) Downloading 'SRR1198762'... 2020-06-21T12:12:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:14:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:14:42 prefetch.2.10.7: 1) 'SRR1198762' was downloaded successfully Read 18188898 spots for SRR1198762/SRR1198762.sra Written 18188898 spots for SRR1198762/SRR1198762.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: 00:03:27 18188898 reads; of these: 18188898 (100.00%) were unpaired; of these: 466022 (2.56%) aligned 0 times 15986547 (87.89%) aligned exactly 1 time 1736329 (9.55%) aligned >1 times 97.44% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 9036635 / 17722876 = 0.5099 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 21:22:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.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 21:22:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:38: 1000000 INFO @ Sun, 21 Jun 2020 21:22:43: 2000000 INFO @ Sun, 21 Jun 2020 21:22:48: 3000000 INFO @ Sun, 21 Jun 2020 21:22:53: 4000000 INFO @ Sun, 21 Jun 2020 21:22:58: 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 21:23:03: 6000000 INFO @ Sun, 21 Jun 2020 21:23:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.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 21:23:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:09: 7000000 INFO @ Sun, 21 Jun 2020 21:23:09: 1000000 INFO @ Sun, 21 Jun 2020 21:23:14: 2000000 INFO @ Sun, 21 Jun 2020 21:23:14: 8000000 INFO @ Sun, 21 Jun 2020 21:23:18: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:23:18: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:23:18: #1 total tags in treatment: 8686241 INFO @ Sun, 21 Jun 2020 21:23:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:18: #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 21:23:19: #1 tags after filtering in treatment: 8686122 INFO @ Sun, 21 Jun 2020 21:23:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:20: #2 number of paired peaks: 6332 INFO @ Sun, 21 Jun 2020 21:23:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:20: 3000000 INFO @ Sun, 21 Jun 2020 21:23:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:20: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 21:23:20: #2 alternative fragment length(s) may be 3 bps INFO @ Sun, 21 Jun 2020 21:23:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.05_model.r WARNING @ Sun, 21 Jun 2020 21:23:20: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:23:20: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sun, 21 Jun 2020 21:23:20: #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 21:23:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:25: 4000000 INFO @ Sun, 21 Jun 2020 21:23:30: 5000000 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 21:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.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 21:23:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:36: 6000000 INFO @ Sun, 21 Jun 2020 21:23:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:39: 1000000 INFO @ Sun, 21 Jun 2020 21:23:41: 7000000 INFO @ Sun, 21 Jun 2020 21:23:44: 2000000 INFO @ Sun, 21 Jun 2020 21:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.05_summits.bed INFO @ Sun, 21 Jun 2020 21:23:44: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:23:47: 8000000 INFO @ Sun, 21 Jun 2020 21:23:50: 3000000 INFO @ Sun, 21 Jun 2020 21:23:51: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:23:51: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:23:51: #1 total tags in treatment: 8686241 INFO @ Sun, 21 Jun 2020 21:23:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:51: #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 21:23:52: #1 tags after filtering in treatment: 8686122 INFO @ Sun, 21 Jun 2020 21:23:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:52: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:52: #2 number of paired peaks: 6332 INFO @ Sun, 21 Jun 2020 21:23:52: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:53: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:53: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:53: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:53: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 21:23:53: #2 alternative fragment length(s) may be 3 bps INFO @ Sun, 21 Jun 2020 21:23:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.10_model.r WARNING @ Sun, 21 Jun 2020 21:23:53: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:23:53: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sun, 21 Jun 2020 21:23:53: #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 21:23:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:55: 4000000 INFO @ Sun, 21 Jun 2020 21:24:00: 5000000 INFO @ Sun, 21 Jun 2020 21:24:06: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:24:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:24:11: 7000000 INFO @ Sun, 21 Jun 2020 21:24:16: 8000000 INFO @ Sun, 21 Jun 2020 21:24:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.10_summits.bed INFO @ Sun, 21 Jun 2020 21:24:17: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:24:20: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:24:20: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:24:20: #1 total tags in treatment: 8686241 INFO @ Sun, 21 Jun 2020 21:24:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:24:20: #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 21:24:20: #1 tags after filtering in treatment: 8686122 INFO @ Sun, 21 Jun 2020 21:24:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:24:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:24:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:24:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:24:21: #2 number of paired peaks: 6332 INFO @ Sun, 21 Jun 2020 21:24:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:24:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:24:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:24:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:24:21: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 21:24:21: #2 alternative fragment length(s) may be 3 bps INFO @ Sun, 21 Jun 2020 21:24:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.20_model.r WARNING @ Sun, 21 Jun 2020 21:24:21: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:24:21: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sun, 21 Jun 2020 21:24:21: #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 21:24:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:24:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:24:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495257/SRX495257.20_summits.bed INFO @ Sun, 21 Jun 2020 21:24:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling