Job ID = 6498620 SRX = SRX645129 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:47:37 prefetch.2.10.7: 1) Downloading 'SRR1505729'... 2020-06-25T23:47:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:56:23 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:56:23 prefetch.2.10.7: 1) 'SRR1505729' was downloaded successfully Read 32790775 spots for SRR1505729/SRR1505729.sra Written 32790775 spots for SRR1505729/SRR1505729.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: 00:14:30 32790775 reads; of these: 32790775 (100.00%) were unpaired; of these: 18465051 (56.31%) aligned 0 times 10919196 (33.30%) aligned exactly 1 time 3406528 (10.39%) aligned >1 times 43.69% overall alignment rate Time searching: 00:14:30 Overall time: 00:14:30 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 8 files... [bam_rmdupse_core] 10646305 / 14325724 = 0.7432 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 09:17:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.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 09:17:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:17:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:17:52: 1000000 INFO @ Fri, 26 Jun 2020 09:18:00: 2000000 INFO @ Fri, 26 Jun 2020 09:18:08: 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 09:18:13: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:18:13: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:18:13: #1 total tags in treatment: 3679419 INFO @ Fri, 26 Jun 2020 09:18:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:18:13: #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 09:18:13: #1 tags after filtering in treatment: 3679419 INFO @ Fri, 26 Jun 2020 09:18:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:18:13: #1 finished! INFO @ Fri, 26 Jun 2020 09:18:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:18:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:18:14: #2 number of paired peaks: 1961 INFO @ Fri, 26 Jun 2020 09:18:14: start model_add_line... INFO @ Fri, 26 Jun 2020 09:18:14: start X-correlation... INFO @ Fri, 26 Jun 2020 09:18:14: end of X-cor INFO @ Fri, 26 Jun 2020 09:18:14: #2 finished! INFO @ Fri, 26 Jun 2020 09:18:14: #2 predicted fragment length is 90 bps INFO @ Fri, 26 Jun 2020 09:18:14: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 26 Jun 2020 09:18:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.05_model.r WARNING @ Fri, 26 Jun 2020 09:18:14: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:18:14: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 26 Jun 2020 09:18:14: #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 09:18:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:18:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:18:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.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 09:18:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:18:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:18:21: 1000000 INFO @ Fri, 26 Jun 2020 09:18:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:18:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.05_summits.bed INFO @ Fri, 26 Jun 2020 09:18:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2535 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:18:29: 2000000 INFO @ Fri, 26 Jun 2020 09:18:37: 3000000 BedGraph に変換中... INFO @ Fri, 26 Jun 2020 09:18:42: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:18:42: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:18:42: #1 total tags in treatment: 3679419 INFO @ Fri, 26 Jun 2020 09:18:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:18:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 09:18:42: #1 tags after filtering in treatment: 3679419 INFO @ Fri, 26 Jun 2020 09:18:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:18:42: #1 finished! INFO @ Fri, 26 Jun 2020 09:18:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:18:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:18:42: #2 number of paired peaks: 1961 INFO @ Fri, 26 Jun 2020 09:18:42: start model_add_line... INFO @ Fri, 26 Jun 2020 09:18:42: start X-correlation... INFO @ Fri, 26 Jun 2020 09:18:42: end of X-cor INFO @ Fri, 26 Jun 2020 09:18:42: #2 finished! INFO @ Fri, 26 Jun 2020 09:18:42: #2 predicted fragment length is 90 bps INFO @ Fri, 26 Jun 2020 09:18:42: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 26 Jun 2020 09:18:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.10_model.r WARNING @ Fri, 26 Jun 2020 09:18:42: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:18:42: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 26 Jun 2020 09:18:42: #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 09:18:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:18:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:18:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.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 09:18:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:18:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:18:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:18:51: 1000000 INFO @ Fri, 26 Jun 2020 09:18:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:18:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:18:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.10_summits.bed INFO @ Fri, 26 Jun 2020 09:18:55: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1217 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:18:59: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:19:06: 3000000 INFO @ Fri, 26 Jun 2020 09:19:12: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:19:12: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:19:12: #1 total tags in treatment: 3679419 INFO @ Fri, 26 Jun 2020 09:19:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:19:12: #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 09:19:12: #1 tags after filtering in treatment: 3679419 INFO @ Fri, 26 Jun 2020 09:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:19:12: #1 finished! INFO @ Fri, 26 Jun 2020 09:19:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:19:12: #2 number of paired peaks: 1961 INFO @ Fri, 26 Jun 2020 09:19:12: start model_add_line... INFO @ Fri, 26 Jun 2020 09:19:12: start X-correlation... INFO @ Fri, 26 Jun 2020 09:19:12: end of X-cor INFO @ Fri, 26 Jun 2020 09:19:12: #2 finished! INFO @ Fri, 26 Jun 2020 09:19:12: #2 predicted fragment length is 90 bps INFO @ Fri, 26 Jun 2020 09:19:12: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 26 Jun 2020 09:19:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.20_model.r WARNING @ Fri, 26 Jun 2020 09:19:12: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:19:12: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 26 Jun 2020 09:19:12: #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 09:19:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:19:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:19:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:19:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:19:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:19:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645129/SRX645129.20_summits.bed INFO @ Fri, 26 Jun 2020 09:19:25: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 2 millis CompletedMACS2peakCalling