Job ID = 6458342 SRX = SRX5011088 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:27:22 prefetch.2.10.7: 1) Downloading 'SRR8191537'... 2020-06-21T12:27:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:30:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:30:03 prefetch.2.10.7: 1) 'SRR8191537' was downloaded successfully Read 23583829 spots for SRR8191537/SRR8191537.sra Written 23583829 spots for SRR8191537/SRR8191537.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: 00:05:19 23583829 reads; of these: 23583829 (100.00%) were unpaired; of these: 4344925 (18.42%) aligned 0 times 15425750 (65.41%) aligned exactly 1 time 3813154 (16.17%) aligned >1 times 81.58% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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] 8947199 / 19238904 = 0.4651 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 21:40:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.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 21:40:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:24: 1000000 INFO @ Sun, 21 Jun 2020 21:40:29: 2000000 INFO @ Sun, 21 Jun 2020 21:40:35: 3000000 INFO @ Sun, 21 Jun 2020 21:40:41: 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 @ Sun, 21 Jun 2020 21:40:47: 5000000 INFO @ Sun, 21 Jun 2020 21:40:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.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 21:40:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:53: 6000000 INFO @ Sun, 21 Jun 2020 21:40:54: 1000000 INFO @ Sun, 21 Jun 2020 21:40:59: 7000000 INFO @ Sun, 21 Jun 2020 21:41:01: 2000000 INFO @ Sun, 21 Jun 2020 21:41:06: 8000000 INFO @ Sun, 21 Jun 2020 21:41:07: 3000000 INFO @ Sun, 21 Jun 2020 21:41:13: 9000000 INFO @ Sun, 21 Jun 2020 21:41:14: 4000000 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 21:41:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.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 21:41:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:20: 10000000 INFO @ Sun, 21 Jun 2020 21:41:21: 5000000 INFO @ Sun, 21 Jun 2020 21:41:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:41:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:41:22: #1 total tags in treatment: 10291705 INFO @ Sun, 21 Jun 2020 21:41:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:22: #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 21:41:22: #1 tags after filtering in treatment: 10291587 INFO @ Sun, 21 Jun 2020 21:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:23: #2 number of paired peaks: 3141 INFO @ Sun, 21 Jun 2020 21:41:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:24: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 21:41:24: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 21:41:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.05_model.r INFO @ Sun, 21 Jun 2020 21:41:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:25: 1000000 INFO @ Sun, 21 Jun 2020 21:41:28: 6000000 INFO @ Sun, 21 Jun 2020 21:41:32: 2000000 INFO @ Sun, 21 Jun 2020 21:41:34: 7000000 INFO @ Sun, 21 Jun 2020 21:41:38: 3000000 INFO @ Sun, 21 Jun 2020 21:41:41: 8000000 INFO @ Sun, 21 Jun 2020 21:41:45: 4000000 INFO @ Sun, 21 Jun 2020 21:41:48: 9000000 INFO @ Sun, 21 Jun 2020 21:41:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:52: 5000000 INFO @ Sun, 21 Jun 2020 21:41:55: 10000000 INFO @ Sun, 21 Jun 2020 21:41:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:41:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:41:57: #1 total tags in treatment: 10291705 INFO @ Sun, 21 Jun 2020 21:41:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:57: #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 21:41:57: #1 tags after filtering in treatment: 10291587 INFO @ Sun, 21 Jun 2020 21:41:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:58: #2 number of paired peaks: 3141 INFO @ Sun, 21 Jun 2020 21:41:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:58: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 21:41:58: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 21:41:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.10_model.r INFO @ Sun, 21 Jun 2020 21:41:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:59: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.05_summits.bed INFO @ Sun, 21 Jun 2020 21:42:04: Done! pass1 - making usageList (404 chroms): 2 millis pass2 - checking and writing primary data (10029 records, 4 fields): 21 millis INFO @ Sun, 21 Jun 2020 21:42:05: 7000000 CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:42:11: 8000000 INFO @ Sun, 21 Jun 2020 21:42:17: 9000000 INFO @ Sun, 21 Jun 2020 21:42:23: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:42:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:42:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:42:25: #1 total tags in treatment: 10291705 INFO @ Sun, 21 Jun 2020 21:42:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:25: #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 21:42:25: #1 tags after filtering in treatment: 10291587 INFO @ Sun, 21 Jun 2020 21:42:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:26: #2 number of paired peaks: 3141 INFO @ Sun, 21 Jun 2020 21:42:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:26: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 21:42:26: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 21:42:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.20_model.r INFO @ Sun, 21 Jun 2020 21:42:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.10_summits.bed INFO @ Sun, 21 Jun 2020 21:42:39: Done! pass1 - making usageList (320 chroms): 2 millis pass2 - checking and writing primary data (6881 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:42:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011088/SRX5011088.20_summits.bed INFO @ Sun, 21 Jun 2020 21:43:06: Done! pass1 - making usageList (232 chroms): 1 millis pass2 - checking and writing primary data (3720 records, 4 fields): 11 millis CompletedMACS2peakCalling