Job ID = 6459862 SRX = SRX914958 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:37:58 prefetch.2.10.7: 1) Downloading 'SRR1873268'... 2020-06-21T13:37:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:41:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:41:54 prefetch.2.10.7: 1) 'SRR1873268' was downloaded successfully Read 26547518 spots for SRR1873268/SRR1873268.sra Written 26547518 spots for SRR1873268/SRR1873268.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: 00:03:28 26547518 reads; of these: 26547518 (100.00%) were unpaired; of these: 12669307 (47.72%) aligned 0 times 12245343 (46.13%) aligned exactly 1 time 1632868 (6.15%) aligned >1 times 52.28% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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_rmdupse_core] 11553816 / 13878211 = 0.8325 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 22:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.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 22:49:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:49:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:49:16: 1000000 INFO @ Sun, 21 Jun 2020 22:49:22: 2000000 INFO @ Sun, 21 Jun 2020 22:49:24: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:49:24: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:49:24: #1 total tags in treatment: 2324395 INFO @ Sun, 21 Jun 2020 22:49:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:49:24: #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 22:49:24: #1 tags after filtering in treatment: 2324222 INFO @ Sun, 21 Jun 2020 22:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:49:24: #1 finished! INFO @ Sun, 21 Jun 2020 22:49:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:49:25: #2 number of paired peaks: 1751 INFO @ Sun, 21 Jun 2020 22:49:25: start model_add_line... INFO @ Sun, 21 Jun 2020 22:49:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:49:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:49:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:49:25: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 22:49:25: #2 alternative fragment length(s) may be 3,135 bps INFO @ Sun, 21 Jun 2020 22:49:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.05_model.r INFO @ Sun, 21 Jun 2020 22:49:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:49:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:49:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:49:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:49:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.05_summits.bed INFO @ Sun, 21 Jun 2020 22:49:34: Done! pass1 - making usageList (152 chroms): 1 millis pass2 - checking and writing primary data (470 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 22:49:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.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 22:49:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:49:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:49:46: 1000000 INFO @ Sun, 21 Jun 2020 22:49:52: 2000000 INFO @ Sun, 21 Jun 2020 22:49:54: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:49:54: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:49:54: #1 total tags in treatment: 2324395 INFO @ Sun, 21 Jun 2020 22:49:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:49:54: #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 22:49:54: #1 tags after filtering in treatment: 2324222 INFO @ Sun, 21 Jun 2020 22:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:49:54: #1 finished! INFO @ Sun, 21 Jun 2020 22:49:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:49:55: #2 number of paired peaks: 1751 INFO @ Sun, 21 Jun 2020 22:49:55: start model_add_line... INFO @ Sun, 21 Jun 2020 22:49:55: start X-correlation... INFO @ Sun, 21 Jun 2020 22:49:55: end of X-cor INFO @ Sun, 21 Jun 2020 22:49:55: #2 finished! INFO @ Sun, 21 Jun 2020 22:49:55: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 22:49:55: #2 alternative fragment length(s) may be 3,135 bps INFO @ Sun, 21 Jun 2020 22:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.10_model.r INFO @ Sun, 21 Jun 2020 22:49:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:50:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:50:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:50:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:50:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.10_summits.bed INFO @ Sun, 21 Jun 2020 22:50:04: Done! pass1 - making usageList (113 chroms): 1 millis pass2 - checking and writing primary data (279 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 22:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.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 22:50:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:50:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:50:16: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:50:23: 2000000 INFO @ Sun, 21 Jun 2020 22:50:25: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:50:25: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:50:25: #1 total tags in treatment: 2324395 INFO @ Sun, 21 Jun 2020 22:50:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:50:25: #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 22:50:25: #1 tags after filtering in treatment: 2324222 INFO @ Sun, 21 Jun 2020 22:50:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:50:25: #1 finished! INFO @ Sun, 21 Jun 2020 22:50:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:50:25: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:50:25: #2 number of paired peaks: 1751 INFO @ Sun, 21 Jun 2020 22:50:25: start model_add_line... INFO @ Sun, 21 Jun 2020 22:50:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:50:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:50:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:50:25: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 22:50:25: #2 alternative fragment length(s) may be 3,135 bps INFO @ Sun, 21 Jun 2020 22:50:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.20_model.r INFO @ Sun, 21 Jun 2020 22:50:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:50:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:50:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:50:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:50:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:50:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914958/SRX914958.20_summits.bed INFO @ Sun, 21 Jun 2020 22:50:35: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (112 records, 4 fields): 5 millis CompletedMACS2peakCalling