Job ID = 6498753 SRX = SRX750076 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:51:52 prefetch.2.10.7: 1) Downloading 'SRR1638764'... 2020-06-25T23:51:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:54:11 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:54:11 prefetch.2.10.7: 'SRR1638764' is valid 2020-06-25T23:54:11 prefetch.2.10.7: 1) 'SRR1638764' was downloaded successfully Read 14418185 spots for SRR1638764/SRR1638764.sra Written 14418185 spots for SRR1638764/SRR1638764.sra 2020-06-25T23:55:08 prefetch.2.10.7: 1) Downloading 'SRR1638765'... 2020-06-25T23:55:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:57:38 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:57:38 prefetch.2.10.7: 1) 'SRR1638765' was downloaded successfully Read 18362894 spots for SRR1638765/SRR1638765.sra Written 18362894 spots for SRR1638765/SRR1638765.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: 00:10:34 32781079 reads; of these: 32781079 (100.00%) were unpaired; of these: 3243856 (9.90%) aligned 0 times 25464000 (77.68%) aligned exactly 1 time 4073223 (12.43%) aligned >1 times 90.10% overall alignment rate Time searching: 00:10:34 Overall time: 00:10:34 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 16 files... [bam_rmdupse_core] 19685768 / 29537223 = 0.6665 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 09:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.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 09:15:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:15:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:15:24: 1000000 INFO @ Fri, 26 Jun 2020 09:15:30: 2000000 INFO @ Fri, 26 Jun 2020 09:15:36: 3000000 INFO @ Fri, 26 Jun 2020 09:15:41: 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 @ Fri, 26 Jun 2020 09:15:47: 5000000 INFO @ Fri, 26 Jun 2020 09:15:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.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 09:15:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:15:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:15:53: 6000000 INFO @ Fri, 26 Jun 2020 09:15:56: 1000000 INFO @ Fri, 26 Jun 2020 09:16:00: 7000000 INFO @ Fri, 26 Jun 2020 09:16:04: 2000000 INFO @ Fri, 26 Jun 2020 09:16:07: 8000000 INFO @ Fri, 26 Jun 2020 09:16:11: 3000000 INFO @ Fri, 26 Jun 2020 09:16:13: 9000000 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 @ Fri, 26 Jun 2020 09:16:18: 4000000 INFO @ Fri, 26 Jun 2020 09:16:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.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 09:16:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:16:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:16:19: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:16:19: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:16:19: #1 total tags in treatment: 9851455 INFO @ Fri, 26 Jun 2020 09:16:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:16:19: #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 09:16:19: #1 tags after filtering in treatment: 9851455 INFO @ Fri, 26 Jun 2020 09:16:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:16:19: #1 finished! INFO @ Fri, 26 Jun 2020 09:16:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:16:20: #2 number of paired peaks: 7118 INFO @ Fri, 26 Jun 2020 09:16:20: start model_add_line... INFO @ Fri, 26 Jun 2020 09:16:20: start X-correlation... INFO @ Fri, 26 Jun 2020 09:16:20: end of X-cor INFO @ Fri, 26 Jun 2020 09:16:20: #2 finished! INFO @ Fri, 26 Jun 2020 09:16:20: #2 predicted fragment length is 159 bps INFO @ Fri, 26 Jun 2020 09:16:20: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 26 Jun 2020 09:16:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.05_model.r INFO @ Fri, 26 Jun 2020 09:16:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:16:25: 1000000 INFO @ Fri, 26 Jun 2020 09:16:26: 5000000 INFO @ Fri, 26 Jun 2020 09:16:32: 2000000 INFO @ Fri, 26 Jun 2020 09:16:33: 6000000 INFO @ Fri, 26 Jun 2020 09:16:39: 3000000 INFO @ Fri, 26 Jun 2020 09:16:41: 7000000 INFO @ Fri, 26 Jun 2020 09:16:45: 4000000 INFO @ Fri, 26 Jun 2020 09:16:48: 8000000 INFO @ Fri, 26 Jun 2020 09:16:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:16:52: 5000000 INFO @ Fri, 26 Jun 2020 09:16:55: 9000000 INFO @ Fri, 26 Jun 2020 09:16:59: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:17:02: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:17:02: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:17:02: #1 total tags in treatment: 9851455 INFO @ Fri, 26 Jun 2020 09:17:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:17:02: #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 09:17:02: #1 tags after filtering in treatment: 9851455 INFO @ Fri, 26 Jun 2020 09:17:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:17:02: #1 finished! INFO @ Fri, 26 Jun 2020 09:17:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:17:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:17:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.05_summits.bed INFO @ Fri, 26 Jun 2020 09:17:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7816 records, 4 fields): 9 millis INFO @ Fri, 26 Jun 2020 09:17:03: #2 number of paired peaks: 7118 INFO @ Fri, 26 Jun 2020 09:17:03: start model_add_line... CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:17:03: start X-correlation... INFO @ Fri, 26 Jun 2020 09:17:03: end of X-cor INFO @ Fri, 26 Jun 2020 09:17:03: #2 finished! INFO @ Fri, 26 Jun 2020 09:17:03: #2 predicted fragment length is 159 bps INFO @ Fri, 26 Jun 2020 09:17:03: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 26 Jun 2020 09:17:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.10_model.r INFO @ Fri, 26 Jun 2020 09:17:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:17:05: 7000000 INFO @ Fri, 26 Jun 2020 09:17:11: 8000000 INFO @ Fri, 26 Jun 2020 09:17:17: 9000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:17:22: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:17:22: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:17:22: #1 total tags in treatment: 9851455 INFO @ Fri, 26 Jun 2020 09:17:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:17:22: #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 09:17:23: #1 tags after filtering in treatment: 9851455 INFO @ Fri, 26 Jun 2020 09:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:17:23: #1 finished! INFO @ Fri, 26 Jun 2020 09:17:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:17:24: #2 number of paired peaks: 7118 INFO @ Fri, 26 Jun 2020 09:17:24: start model_add_line... INFO @ Fri, 26 Jun 2020 09:17:24: start X-correlation... INFO @ Fri, 26 Jun 2020 09:17:24: end of X-cor INFO @ Fri, 26 Jun 2020 09:17:24: #2 finished! INFO @ Fri, 26 Jun 2020 09:17:24: #2 predicted fragment length is 159 bps INFO @ Fri, 26 Jun 2020 09:17:24: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 26 Jun 2020 09:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.20_model.r INFO @ Fri, 26 Jun 2020 09:17:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:17:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.10_summits.bed INFO @ Fri, 26 Jun 2020 09:17:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6142 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:17:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750076/SRX750076.20_summits.bed INFO @ Fri, 26 Jun 2020 09:18:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4219 records, 4 fields): 5 millis CompletedMACS2peakCalling