Job ID = 6453796 SRX = SRX1490788 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:37:11 prefetch.2.10.7: 1) Downloading 'SRR3031655'... 2020-06-21T08:37:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:39:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:39:39 prefetch.2.10.7: 'SRR3031655' is valid 2020-06-21T08:39:39 prefetch.2.10.7: 1) 'SRR3031655' was downloaded successfully Read 13296061 spots for SRR3031655/SRR3031655.sra Written 13296061 spots for SRR3031655/SRR3031655.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: 00:03:27 13296061 reads; of these: 13296061 (100.00%) were unpaired; of these: 2835427 (21.33%) aligned 0 times 6337538 (47.66%) aligned exactly 1 time 4123096 (31.01%) aligned >1 times 78.67% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 8695044 / 10460634 = 0.8312 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 17:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.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 17:45:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:53: 1000000 INFO @ Sun, 21 Jun 2020 17:45:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:45:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:45:59: #1 total tags in treatment: 1765590 INFO @ Sun, 21 Jun 2020 17:45:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:59: #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 17:45:59: #1 tags after filtering in treatment: 1765524 INFO @ Sun, 21 Jun 2020 17:45:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:00: #2 number of paired peaks: 1854 INFO @ Sun, 21 Jun 2020 17:46:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:00: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 17:46:00: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 17:46:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.05_model.r INFO @ Sun, 21 Jun 2020 17:46:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:46:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:46:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:46:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.05_summits.bed INFO @ Sun, 21 Jun 2020 17:46:07: Done! pass1 - making usageList (358 chroms): 2 millis pass2 - checking and writing primary data (2504 records, 4 fields): 14 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 17:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.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 17:46:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:21: 1000000 INFO @ Sun, 21 Jun 2020 17:46:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:46:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:46:26: #1 total tags in treatment: 1765590 INFO @ Sun, 21 Jun 2020 17:46:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:26: #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 17:46:26: #1 tags after filtering in treatment: 1765524 INFO @ Sun, 21 Jun 2020 17:46:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:26: #2 number of paired peaks: 1854 INFO @ Sun, 21 Jun 2020 17:46:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:27: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 17:46:27: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 17:46:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.10_model.r INFO @ Sun, 21 Jun 2020 17:46:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.10_summits.bed INFO @ Sun, 21 Jun 2020 17:46:34: Done! pass1 - making usageList (190 chroms): 1 millis pass2 - checking and writing primary data (1357 records, 4 fields): 7 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 17:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.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 17:46:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:45: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:46:52: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:46:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:46:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:46:57: #1 total tags in treatment: 1765590 INFO @ Sun, 21 Jun 2020 17:46:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:57: #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 17:46:57: #1 tags after filtering in treatment: 1765524 INFO @ Sun, 21 Jun 2020 17:46:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:57: #2 number of paired peaks: 1854 INFO @ Sun, 21 Jun 2020 17:46:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:57: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 17:46:57: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 17:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.20_model.r INFO @ Sun, 21 Jun 2020 17:46:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490788/SRX1490788.20_summits.bed INFO @ Sun, 21 Jun 2020 17:47:05: Done! pass1 - making usageList (151 chroms): 3 millis pass2 - checking and writing primary data (824 records, 4 fields): 6 millis CompletedMACS2peakCalling