Job ID = 6453008 SRX = SRX097621 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:14:03 prefetch.2.10.7: 1) Downloading 'SRR345572'... 2020-06-21T08:14:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:20:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:20:11 prefetch.2.10.7: 1) 'SRR345572' was downloaded successfully Read 37304434 spots for SRR345572/SRR345572.sra Written 37304434 spots for SRR345572/SRR345572.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: 00:09:41 37304434 reads; of these: 37304434 (100.00%) were unpaired; of these: 1337824 (3.59%) aligned 0 times 25612689 (68.66%) aligned exactly 1 time 10353921 (27.76%) aligned >1 times 96.41% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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] 26816046 / 35966610 = 0.7456 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 17:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.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 17:37:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:06: 1000000 INFO @ Sun, 21 Jun 2020 17:37:12: 2000000 INFO @ Sun, 21 Jun 2020 17:37:18: 3000000 INFO @ Sun, 21 Jun 2020 17:37:24: 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 @ Sun, 21 Jun 2020 17:37:30: 5000000 INFO @ Sun, 21 Jun 2020 17:37:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.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 17:37:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:35: 6000000 INFO @ Sun, 21 Jun 2020 17:37:36: 1000000 INFO @ Sun, 21 Jun 2020 17:37:41: 2000000 INFO @ Sun, 21 Jun 2020 17:37:42: 7000000 INFO @ Sun, 21 Jun 2020 17:37:45: 3000000 INFO @ Sun, 21 Jun 2020 17:37:47: 8000000 INFO @ Sun, 21 Jun 2020 17:37:50: 4000000 INFO @ Sun, 21 Jun 2020 17:37:52: 9000000 INFO @ Sun, 21 Jun 2020 17:37:53: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:37:53: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:37:53: #1 total tags in treatment: 9150564 INFO @ Sun, 21 Jun 2020 17:37:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:53: #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 17:37:53: #1 tags after filtering in treatment: 9150520 INFO @ Sun, 21 Jun 2020 17:37:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:54: #2 number of paired peaks: 4089 INFO @ Sun, 21 Jun 2020 17:37:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:54: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:37:54: #2 alternative fragment length(s) may be 2,75 bps INFO @ Sun, 21 Jun 2020 17:37:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.05_model.r WARNING @ Sun, 21 Jun 2020 17:37:54: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:37:54: #2 You may need to consider one of the other alternative d(s): 2,75 WARNING @ Sun, 21 Jun 2020 17:37:54: #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 17:37:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:37:55: 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 17:38:00: 6000000 INFO @ Sun, 21 Jun 2020 17:38:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.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 17:38:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:05: 7000000 INFO @ Sun, 21 Jun 2020 17:38:06: 1000000 INFO @ Sun, 21 Jun 2020 17:38:10: 8000000 INFO @ Sun, 21 Jun 2020 17:38:10: 2000000 INFO @ Sun, 21 Jun 2020 17:38:15: 9000000 INFO @ Sun, 21 Jun 2020 17:38:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:15: 3000000 INFO @ Sun, 21 Jun 2020 17:38:15: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:38:15: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:38:15: #1 total tags in treatment: 9150564 INFO @ Sun, 21 Jun 2020 17:38:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:15: #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 17:38:16: #1 tags after filtering in treatment: 9150520 INFO @ Sun, 21 Jun 2020 17:38:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:16: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:17: #2 number of paired peaks: 4089 INFO @ Sun, 21 Jun 2020 17:38:17: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:17: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:38:17: #2 alternative fragment length(s) may be 2,75 bps INFO @ Sun, 21 Jun 2020 17:38:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.10_model.r WARNING @ Sun, 21 Jun 2020 17:38:17: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:38:17: #2 You may need to consider one of the other alternative d(s): 2,75 WARNING @ Sun, 21 Jun 2020 17:38:17: #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 17:38:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:20: 4000000 INFO @ Sun, 21 Jun 2020 17:38:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.05_summits.bed INFO @ Sun, 21 Jun 2020 17:38:24: Done! INFO @ Sun, 21 Jun 2020 17:38:25: 5000000 pass1 - making usageList (867 chroms): 1 millis pass2 - checking and writing primary data (4863 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:29: 6000000 INFO @ Sun, 21 Jun 2020 17:38:34: 7000000 INFO @ Sun, 21 Jun 2020 17:38:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:39: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:38:44: 9000000 INFO @ Sun, 21 Jun 2020 17:38:45: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:38:45: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:38:45: #1 total tags in treatment: 9150564 INFO @ Sun, 21 Jun 2020 17:38:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:45: #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 17:38:45: #1 tags after filtering in treatment: 9150520 INFO @ Sun, 21 Jun 2020 17:38:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:45: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:46: #2 number of paired peaks: 4089 INFO @ Sun, 21 Jun 2020 17:38:46: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:46: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:46: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:46: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:46: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:38:46: #2 alternative fragment length(s) may be 2,75 bps INFO @ Sun, 21 Jun 2020 17:38:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.20_model.r WARNING @ Sun, 21 Jun 2020 17:38:46: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:38:46: #2 You may need to consider one of the other alternative d(s): 2,75 WARNING @ Sun, 21 Jun 2020 17:38:46: #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 17:38:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.10_summits.bed INFO @ Sun, 21 Jun 2020 17:38:47: Done! pass1 - making usageList (709 chroms): 1 millis pass2 - checking and writing primary data (2621 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:39:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX097621/SRX097621.20_summits.bed INFO @ Sun, 21 Jun 2020 17:39:15: Done! pass1 - making usageList (545 chroms): 1 millis pass2 - checking and writing primary data (1718 records, 4 fields): 16 millis CompletedMACS2peakCalling