Job ID = 6457098 SRX = SRX4375858 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:38:25 prefetch.2.10.7: 1) Downloading 'SRR7506512'... 2020-06-21T11:38:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:41:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:41:30 prefetch.2.10.7: 'SRR7506512' is valid 2020-06-21T11:41:30 prefetch.2.10.7: 1) 'SRR7506512' was downloaded successfully Read 14076180 spots for SRR7506512/SRR7506512.sra Written 14076180 spots for SRR7506512/SRR7506512.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: 00:02:33 14076180 reads; of these: 14076180 (100.00%) were unpaired; of these: 4100932 (29.13%) aligned 0 times 8305812 (59.01%) aligned exactly 1 time 1669436 (11.86%) aligned >1 times 70.87% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 2506971 / 9975248 = 0.2513 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 20:47:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.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 20:47:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:47:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:47:40: 1000000 INFO @ Sun, 21 Jun 2020 20:47:45: 2000000 INFO @ Sun, 21 Jun 2020 20:47:49: 3000000 INFO @ Sun, 21 Jun 2020 20:47:54: 4000000 INFO @ Sun, 21 Jun 2020 20:47:59: 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 20:48:03: 6000000 INFO @ Sun, 21 Jun 2020 20:48:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.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 20:48:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:48:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:48:08: 7000000 INFO @ Sun, 21 Jun 2020 20:48:09: 1000000 INFO @ Sun, 21 Jun 2020 20:48:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:48:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:48:10: #1 total tags in treatment: 7468277 INFO @ Sun, 21 Jun 2020 20:48:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:48:10: #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 20:48:11: #1 tags after filtering in treatment: 7467999 INFO @ Sun, 21 Jun 2020 20:48:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:48:11: #1 finished! INFO @ Sun, 21 Jun 2020 20:48:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:48:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:48:12: #2 number of paired peaks: 8151 INFO @ Sun, 21 Jun 2020 20:48:12: start model_add_line... INFO @ Sun, 21 Jun 2020 20:48:12: start X-correlation... INFO @ Sun, 21 Jun 2020 20:48:12: end of X-cor INFO @ Sun, 21 Jun 2020 20:48:12: #2 finished! INFO @ Sun, 21 Jun 2020 20:48:12: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 20:48:12: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 20:48:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.05_model.r INFO @ Sun, 21 Jun 2020 20:48:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:48:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:48:14: 2000000 INFO @ Sun, 21 Jun 2020 20:48:18: 3000000 INFO @ Sun, 21 Jun 2020 20:48:23: 4000000 INFO @ Sun, 21 Jun 2020 20:48:27: 5000000 INFO @ Sun, 21 Jun 2020 20:48:32: 6000000 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 20:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.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 20:48:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:48:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:48:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:48:37: 7000000 INFO @ Sun, 21 Jun 2020 20:48:39: 1000000 INFO @ Sun, 21 Jun 2020 20:48:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:48:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:48:39: #1 total tags in treatment: 7468277 INFO @ Sun, 21 Jun 2020 20:48:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:48:39: #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 20:48:40: #1 tags after filtering in treatment: 7467999 INFO @ Sun, 21 Jun 2020 20:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:48:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:48:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:48:41: #2 number of paired peaks: 8151 INFO @ Sun, 21 Jun 2020 20:48:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:48:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:48:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:48:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:48:41: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 20:48:41: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 20:48:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.10_model.r INFO @ Sun, 21 Jun 2020 20:48:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:48:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:48:44: 2000000 INFO @ Sun, 21 Jun 2020 20:48:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:48:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:48:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.05_summits.bed INFO @ Sun, 21 Jun 2020 20:48:46: Done! pass1 - making usageList (173 chroms): 4 millis pass2 - checking and writing primary data (8460 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:48:48: 3000000 INFO @ Sun, 21 Jun 2020 20:48:53: 4000000 INFO @ Sun, 21 Jun 2020 20:48:58: 5000000 INFO @ Sun, 21 Jun 2020 20:49:02: 6000000 INFO @ Sun, 21 Jun 2020 20:49:04: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:49:07: 7000000 INFO @ Sun, 21 Jun 2020 20:49:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:49:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:49:09: #1 total tags in treatment: 7468277 INFO @ Sun, 21 Jun 2020 20:49:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:49:09: #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 20:49:10: #1 tags after filtering in treatment: 7467999 INFO @ Sun, 21 Jun 2020 20:49:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:49:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:49:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:49:11: #2 number of paired peaks: 8151 INFO @ Sun, 21 Jun 2020 20:49:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:49:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:49:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:49:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:49:11: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 20:49:11: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 20:49:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.20_model.r INFO @ Sun, 21 Jun 2020 20:49:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:49:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:49:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:49:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:49:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.10_summits.bed INFO @ Sun, 21 Jun 2020 20:49:14: Done! pass1 - making usageList (121 chroms): 1 millis pass2 - checking and writing primary data (6563 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:49:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:49:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:49:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375858/SRX4375858.20_summits.bed INFO @ Sun, 21 Jun 2020 20:49:43: Done! pass1 - making usageList (84 chroms): 1 millis pass2 - checking and writing primary data (4770 records, 4 fields): 8 millis CompletedMACS2peakCalling