Job ID = 8069488 SRX = SRX7191475 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-08T03:33:29 prefetch.2.10.7: 1) Downloading 'SRR10502459'... 2020-08-08T03:33:29 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:45 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:46 prefetch.2.10.7: 'SRR10502459' is valid 2020-08-08T03:34:46 prefetch.2.10.7: 1) 'SRR10502459' was downloaded successfully Read 14261400 spots for SRR10502459/SRR10502459.sra Written 14261400 spots for SRR10502459/SRR10502459.sra fastq に変換しました。 bowtie でマッピング中... Your job 8069886 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:52 14261400 reads; of these: 14261400 (100.00%) were unpaired; of these: 912185 (6.40%) aligned 0 times 10738169 (75.30%) aligned exactly 1 time 2611046 (18.31%) aligned >1 times 93.60% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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 8 files... [bam_rmdupse_core] 1582434 / 13349215 = 0.1185 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 @ Sat, 08 Aug 2020 12:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.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 @ Sat, 08 Aug 2020 12:42:32: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:42:32: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:42:38: 1000000 INFO @ Sat, 08 Aug 2020 12:42:44: 2000000 INFO @ Sat, 08 Aug 2020 12:42:51: 3000000 INFO @ Sat, 08 Aug 2020 12:42:57: 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 @ Sat, 08 Aug 2020 12:43:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.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 @ Sat, 08 Aug 2020 12:43:02: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:43:02: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:43:03: 5000000 INFO @ Sat, 08 Aug 2020 12:43:08: 1000000 INFO @ Sat, 08 Aug 2020 12:43:09: 6000000 INFO @ Sat, 08 Aug 2020 12:43:15: 2000000 INFO @ Sat, 08 Aug 2020 12:43:16: 7000000 INFO @ Sat, 08 Aug 2020 12:43:21: 3000000 INFO @ Sat, 08 Aug 2020 12:43:22: 8000000 INFO @ Sat, 08 Aug 2020 12:43:28: 4000000 INFO @ Sat, 08 Aug 2020 12:43:29: 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 @ Sat, 08 Aug 2020 12:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.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 @ Sat, 08 Aug 2020 12:43:32: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:43:32: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:43:35: 5000000 INFO @ Sat, 08 Aug 2020 12:43:35: 10000000 INFO @ Sat, 08 Aug 2020 12:43:38: 1000000 INFO @ Sat, 08 Aug 2020 12:43:41: 6000000 INFO @ Sat, 08 Aug 2020 12:43:42: 11000000 INFO @ Sat, 08 Aug 2020 12:43:44: 2000000 INFO @ Sat, 08 Aug 2020 12:43:47: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:43:47: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:43:47: #1 total tags in treatment: 11766781 INFO @ Sat, 08 Aug 2020 12:43:47: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:43:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:43:47: #1 tags after filtering in treatment: 11766781 INFO @ Sat, 08 Aug 2020 12:43:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:43:47: #1 finished! INFO @ Sat, 08 Aug 2020 12:43:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:43:48: #2 number of paired peaks: 1634 INFO @ Sat, 08 Aug 2020 12:43:48: start model_add_line... INFO @ Sat, 08 Aug 2020 12:43:48: start X-correlation... INFO @ Sat, 08 Aug 2020 12:43:48: end of X-cor INFO @ Sat, 08 Aug 2020 12:43:48: #2 finished! INFO @ Sat, 08 Aug 2020 12:43:48: #2 predicted fragment length is 220 bps INFO @ Sat, 08 Aug 2020 12:43:48: #2 alternative fragment length(s) may be 220 bps INFO @ Sat, 08 Aug 2020 12:43:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.05_model.r INFO @ Sat, 08 Aug 2020 12:43:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:43:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:43:48: 7000000 INFO @ Sat, 08 Aug 2020 12:43:50: 3000000 INFO @ Sat, 08 Aug 2020 12:43:55: 8000000 INFO @ Sat, 08 Aug 2020 12:43:57: 4000000 INFO @ Sat, 08 Aug 2020 12:44:02: 9000000 INFO @ Sat, 08 Aug 2020 12:44:03: 5000000 INFO @ Sat, 08 Aug 2020 12:44:08: 10000000 INFO @ Sat, 08 Aug 2020 12:44:09: 6000000 INFO @ Sat, 08 Aug 2020 12:44:14: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:44:15: 7000000 INFO @ Sat, 08 Aug 2020 12:44:15: 11000000 INFO @ Sat, 08 Aug 2020 12:44:20: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:44:20: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:44:20: #1 total tags in treatment: 11766781 INFO @ Sat, 08 Aug 2020 12:44:20: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:44:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:44:21: #1 tags after filtering in treatment: 11766781 INFO @ Sat, 08 Aug 2020 12:44:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:44:21: #1 finished! INFO @ Sat, 08 Aug 2020 12:44:21: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:44:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:44:21: 8000000 INFO @ Sat, 08 Aug 2020 12:44:21: #2 number of paired peaks: 1634 INFO @ Sat, 08 Aug 2020 12:44:21: start model_add_line... INFO @ Sat, 08 Aug 2020 12:44:22: start X-correlation... INFO @ Sat, 08 Aug 2020 12:44:22: end of X-cor INFO @ Sat, 08 Aug 2020 12:44:22: #2 finished! INFO @ Sat, 08 Aug 2020 12:44:22: #2 predicted fragment length is 220 bps INFO @ Sat, 08 Aug 2020 12:44:22: #2 alternative fragment length(s) may be 220 bps INFO @ Sat, 08 Aug 2020 12:44:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.10_model.r INFO @ Sat, 08 Aug 2020 12:44:22: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:44:22: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:44:26: 9000000 INFO @ Sat, 08 Aug 2020 12:44:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:44:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:44:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.05_summits.bed INFO @ Sat, 08 Aug 2020 12:44:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7268 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:44:32: 10000000 INFO @ Sat, 08 Aug 2020 12:44:37: 11000000 INFO @ Sat, 08 Aug 2020 12:44:41: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:44:41: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:44:41: #1 total tags in treatment: 11766781 INFO @ Sat, 08 Aug 2020 12:44:41: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:44:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:44:41: #1 tags after filtering in treatment: 11766781 INFO @ Sat, 08 Aug 2020 12:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:44:41: #1 finished! INFO @ Sat, 08 Aug 2020 12:44:41: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:44:42: #2 number of paired peaks: 1634 INFO @ Sat, 08 Aug 2020 12:44:42: start model_add_line... INFO @ Sat, 08 Aug 2020 12:44:42: start X-correlation... INFO @ Sat, 08 Aug 2020 12:44:42: end of X-cor INFO @ Sat, 08 Aug 2020 12:44:42: #2 finished! INFO @ Sat, 08 Aug 2020 12:44:42: #2 predicted fragment length is 220 bps INFO @ Sat, 08 Aug 2020 12:44:42: #2 alternative fragment length(s) may be 220 bps INFO @ Sat, 08 Aug 2020 12:44:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.20_model.r INFO @ Sat, 08 Aug 2020 12:44:42: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:44:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.10_summits.bed INFO @ Sat, 08 Aug 2020 12:45:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4908 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:45:09: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191475/SRX7191475.20_summits.bed INFO @ Sat, 08 Aug 2020 12:45:21: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2908 records, 4 fields): 4 millis CompletedMACS2peakCalling