Job ID = 6457801 SRX = SRX4798846 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:11:19 prefetch.2.10.7: 1) Downloading 'SRR7965223'... 2020-06-21T12:11:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:12:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:12:53 prefetch.2.10.7: 'SRR7965223' is valid 2020-06-21T12:12:53 prefetch.2.10.7: 1) 'SRR7965223' was downloaded successfully Read 14342870 spots for SRR7965223/SRR7965223.sra Written 14342870 spots for SRR7965223/SRR7965223.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: 00:02:37 14342870 reads; of these: 14342870 (100.00%) were unpaired; of these: 2282472 (15.91%) aligned 0 times 11392749 (79.43%) aligned exactly 1 time 667649 (4.65%) aligned >1 times 84.09% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 2682211 / 12060398 = 0.2224 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 21:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.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 21:20:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:36: 1000000 INFO @ Sun, 21 Jun 2020 21:20:41: 2000000 INFO @ Sun, 21 Jun 2020 21:20:47: 3000000 INFO @ Sun, 21 Jun 2020 21:20:52: 4000000 INFO @ Sun, 21 Jun 2020 21:20:57: 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 21:21:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.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 21:21:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:03: 6000000 INFO @ Sun, 21 Jun 2020 21:21:06: 1000000 INFO @ Sun, 21 Jun 2020 21:21:09: 7000000 INFO @ Sun, 21 Jun 2020 21:21:12: 2000000 INFO @ Sun, 21 Jun 2020 21:21:15: 8000000 INFO @ Sun, 21 Jun 2020 21:21:18: 3000000 INFO @ Sun, 21 Jun 2020 21:21:21: 9000000 INFO @ Sun, 21 Jun 2020 21:21:24: 4000000 INFO @ Sun, 21 Jun 2020 21:21:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:21:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:21:24: #1 total tags in treatment: 9378187 INFO @ Sun, 21 Jun 2020 21:21:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:24: #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 21:21:24: #1 tags after filtering in treatment: 9378022 INFO @ Sun, 21 Jun 2020 21:21:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:26: #2 number of paired peaks: 9099 INFO @ Sun, 21 Jun 2020 21:21:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:26: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 21:21:26: #2 alternative fragment length(s) may be 4,174 bps INFO @ Sun, 21 Jun 2020 21:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.05_model.r INFO @ Sun, 21 Jun 2020 21:21:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:26: #3 Pre-compute pvalue-qvalue table... 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 21:21:29: 5000000 INFO @ Sun, 21 Jun 2020 21:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.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 21:21:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:35: 6000000 INFO @ Sun, 21 Jun 2020 21:21:36: 1000000 INFO @ Sun, 21 Jun 2020 21:21:41: 7000000 INFO @ Sun, 21 Jun 2020 21:21:42: 2000000 INFO @ Sun, 21 Jun 2020 21:21:47: 8000000 INFO @ Sun, 21 Jun 2020 21:21:48: 3000000 INFO @ Sun, 21 Jun 2020 21:21:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:21:53: 9000000 INFO @ Sun, 21 Jun 2020 21:21:54: 4000000 INFO @ Sun, 21 Jun 2020 21:21:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:21:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:21:56: #1 total tags in treatment: 9378187 INFO @ Sun, 21 Jun 2020 21:21:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:56: #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 21:21:56: #1 tags after filtering in treatment: 9378022 INFO @ Sun, 21 Jun 2020 21:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:58: #2 number of paired peaks: 9099 INFO @ Sun, 21 Jun 2020 21:21:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:58: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 21:21:58: #2 alternative fragment length(s) may be 4,174 bps INFO @ Sun, 21 Jun 2020 21:21:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.10_model.r INFO @ Sun, 21 Jun 2020 21:21:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:00: 5000000 INFO @ Sun, 21 Jun 2020 21:22:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.05_summits.bed INFO @ Sun, 21 Jun 2020 21:22:03: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (8094 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:22:05: 6000000 INFO @ Sun, 21 Jun 2020 21:22:10: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:22:17: 8000000 INFO @ Sun, 21 Jun 2020 21:22:22: 9000000 INFO @ Sun, 21 Jun 2020 21:22:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:22:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:22:24: #1 total tags in treatment: 9378187 INFO @ Sun, 21 Jun 2020 21:22:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:24: #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 21:22:25: #1 tags after filtering in treatment: 9378022 INFO @ Sun, 21 Jun 2020 21:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:26: #2 number of paired peaks: 9099 INFO @ Sun, 21 Jun 2020 21:22:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:27: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 21:22:27: #2 alternative fragment length(s) may be 4,174 bps INFO @ Sun, 21 Jun 2020 21:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.20_model.r INFO @ Sun, 21 Jun 2020 21:22:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.10_summits.bed INFO @ Sun, 21 Jun 2020 21:22:34: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (4850 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:22:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798846/SRX4798846.20_summits.bed INFO @ Sun, 21 Jun 2020 21:23:02: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (1775 records, 4 fields): 5 millis CompletedMACS2peakCalling