Job ID = 6458590 SRX = SRX5343126 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:41:29 prefetch.2.10.7: 1) Downloading 'SRR8540826'... 2020-06-21T12:41:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:44:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:44:25 prefetch.2.10.7: 'SRR8540826' is valid 2020-06-21T12:44:25 prefetch.2.10.7: 1) 'SRR8540826' was downloaded successfully 2020-06-21T12:44:25 prefetch.2.10.7: 'SRR8540826' has 0 unresolved dependencies Read 20836618 spots for SRR8540826/SRR8540826.sra Written 20836618 spots for SRR8540826/SRR8540826.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: 00:05:33 20836618 reads; of these: 20836618 (100.00%) were unpaired; of these: 3308334 (15.88%) aligned 0 times 15319549 (73.52%) aligned exactly 1 time 2208735 (10.60%) aligned >1 times 84.12% overall alignment rate Time searching: 00:05:33 Overall time: 00:05:33 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] 11187173 / 17528284 = 0.6382 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 21:54:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.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 21:54:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:52: 1000000 INFO @ Sun, 21 Jun 2020 21:54:58: 2000000 INFO @ Sun, 21 Jun 2020 21:55:03: 3000000 INFO @ Sun, 21 Jun 2020 21:55:08: 4000000 INFO @ Sun, 21 Jun 2020 21:55:14: 5000000 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 21:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.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 21:55:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:19: 6000000 INFO @ Sun, 21 Jun 2020 21:55:22: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:55:22: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:55:22: #1 total tags in treatment: 6341111 INFO @ Sun, 21 Jun 2020 21:55:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:22: #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 21:55:22: #1 tags after filtering in treatment: 6341098 INFO @ Sun, 21 Jun 2020 21:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:23: 1000000 INFO @ Sun, 21 Jun 2020 21:55:23: #2 number of paired peaks: 8946 INFO @ Sun, 21 Jun 2020 21:55:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:23: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:23: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:23: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 21:55:23: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 21:55:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.05_model.r INFO @ Sun, 21 Jun 2020 21:55:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:28: 2000000 INFO @ Sun, 21 Jun 2020 21:55:34: 3000000 INFO @ Sun, 21 Jun 2020 21:55:39: 4000000 INFO @ Sun, 21 Jun 2020 21:55:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:44: 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 21:55:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.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 21:55:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.05_summits.bed INFO @ Sun, 21 Jun 2020 21:55:48: Done! pass1 - making usageList (342 chroms): 2 millis pass2 - checking and writing primary data (7528 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:55:50: 6000000 INFO @ Sun, 21 Jun 2020 21:55:53: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:55:53: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:55:53: #1 total tags in treatment: 6341111 INFO @ Sun, 21 Jun 2020 21:55:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:53: #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 21:55:53: #1 tags after filtering in treatment: 6341098 INFO @ Sun, 21 Jun 2020 21:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:53: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:54: 1000000 INFO @ Sun, 21 Jun 2020 21:55:54: #2 number of paired peaks: 8946 INFO @ Sun, 21 Jun 2020 21:55:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:54: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 21:55:54: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 21:55:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.10_model.r INFO @ Sun, 21 Jun 2020 21:55:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:00: 2000000 INFO @ Sun, 21 Jun 2020 21:56:07: 3000000 INFO @ Sun, 21 Jun 2020 21:56:10: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:56:13: 4000000 INFO @ Sun, 21 Jun 2020 21:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.10_summits.bed INFO @ Sun, 21 Jun 2020 21:56:19: Done! pass1 - making usageList (182 chroms): 2 millis pass2 - checking and writing primary data (6565 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:56:19: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:56:26: 6000000 INFO @ Sun, 21 Jun 2020 21:56:28: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:56:28: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:56:28: #1 total tags in treatment: 6341111 INFO @ Sun, 21 Jun 2020 21:56:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:28: #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 21:56:29: #1 tags after filtering in treatment: 6341098 INFO @ Sun, 21 Jun 2020 21:56:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:29: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:30: #2 number of paired peaks: 8946 INFO @ Sun, 21 Jun 2020 21:56:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:30: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 21:56:30: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 21:56:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.20_model.r INFO @ Sun, 21 Jun 2020 21:56:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343126/SRX5343126.20_summits.bed INFO @ Sun, 21 Jun 2020 21:56:55: Done! pass1 - making usageList (122 chroms): 2 millis pass2 - checking and writing primary data (5295 records, 4 fields): 10 millis CompletedMACS2peakCalling