Job ID = 6454977 SRX = SRX2618516 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:44:25 prefetch.2.10.7: 1) Downloading 'SRR5319070'... 2020-06-21T09:44:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:50 prefetch.2.10.7: 'SRR5319070' is valid 2020-06-21T09:46:50 prefetch.2.10.7: 1) 'SRR5319070' was downloaded successfully 2020-06-21T09:46:50 prefetch.2.10.7: 'SRR5319070' has 0 unresolved dependencies Read 22334484 spots for SRR5319070/SRR5319070.sra Written 22334484 spots for SRR5319070/SRR5319070.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: 00:03:53 22334484 reads; of these: 22334484 (100.00%) were unpaired; of these: 7073064 (31.67%) aligned 0 times 13929728 (62.37%) aligned exactly 1 time 1331692 (5.96%) aligned >1 times 68.33% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 3703449 / 15261420 = 0.2427 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 18:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.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 18:55:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:39: 1000000 INFO @ Sun, 21 Jun 2020 18:55:45: 2000000 INFO @ Sun, 21 Jun 2020 18:55:51: 3000000 INFO @ Sun, 21 Jun 2020 18:55:56: 4000000 INFO @ Sun, 21 Jun 2020 18:56:01: 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 18:56:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.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 18:56:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:07: 6000000 INFO @ Sun, 21 Jun 2020 18:56:10: 1000000 INFO @ Sun, 21 Jun 2020 18:56:12: 7000000 INFO @ Sun, 21 Jun 2020 18:56:16: 2000000 INFO @ Sun, 21 Jun 2020 18:56:18: 8000000 INFO @ Sun, 21 Jun 2020 18:56:22: 3000000 INFO @ Sun, 21 Jun 2020 18:56:24: 9000000 INFO @ Sun, 21 Jun 2020 18:56:28: 4000000 INFO @ Sun, 21 Jun 2020 18:56:30: 10000000 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 18:56:33: 5000000 INFO @ Sun, 21 Jun 2020 18:56:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.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 18:56:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:35: 11000000 INFO @ Sun, 21 Jun 2020 18:56:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:56:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:56:39: #1 total tags in treatment: 11557971 INFO @ Sun, 21 Jun 2020 18:56:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:39: #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 18:56:39: 6000000 INFO @ Sun, 21 Jun 2020 18:56:39: #1 tags after filtering in treatment: 11557919 INFO @ Sun, 21 Jun 2020 18:56:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:40: 1000000 INFO @ Sun, 21 Jun 2020 18:56:41: #2 number of paired peaks: 8898 INFO @ Sun, 21 Jun 2020 18:56:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:41: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 18:56:41: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 18:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.05_model.r INFO @ Sun, 21 Jun 2020 18:56:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:45: 7000000 INFO @ Sun, 21 Jun 2020 18:56:46: 2000000 INFO @ Sun, 21 Jun 2020 18:56:50: 8000000 INFO @ Sun, 21 Jun 2020 18:56:51: 3000000 INFO @ Sun, 21 Jun 2020 18:56:56: 9000000 INFO @ Sun, 21 Jun 2020 18:56:57: 4000000 INFO @ Sun, 21 Jun 2020 18:57:02: 10000000 INFO @ Sun, 21 Jun 2020 18:57:03: 5000000 INFO @ Sun, 21 Jun 2020 18:57:08: 11000000 INFO @ Sun, 21 Jun 2020 18:57:08: 6000000 INFO @ Sun, 21 Jun 2020 18:57:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:57:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:57:11: #1 total tags in treatment: 11557971 INFO @ Sun, 21 Jun 2020 18:57:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:11: #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 18:57:12: #1 tags after filtering in treatment: 11557919 INFO @ Sun, 21 Jun 2020 18:57:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:13: #2 number of paired peaks: 8898 INFO @ Sun, 21 Jun 2020 18:57:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:13: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 18:57:13: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 18:57:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.10_model.r INFO @ Sun, 21 Jun 2020 18:57:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:14: 7000000 INFO @ Sun, 21 Jun 2020 18:57:19: 8000000 INFO @ Sun, 21 Jun 2020 18:57:24: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.05_summits.bed INFO @ Sun, 21 Jun 2020 18:57:27: Done! pass1 - making usageList (406 chroms): 2 millis pass2 - checking and writing primary data (8619 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:30: 10000000 INFO @ Sun, 21 Jun 2020 18:57:34: 11000000 INFO @ Sun, 21 Jun 2020 18:57:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:57:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:57:38: #1 total tags in treatment: 11557971 INFO @ Sun, 21 Jun 2020 18:57:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:38: #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 18:57:38: #1 tags after filtering in treatment: 11557919 INFO @ Sun, 21 Jun 2020 18:57:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:39: #2 number of paired peaks: 8898 INFO @ Sun, 21 Jun 2020 18:57:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:40: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 18:57:40: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 18:57:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.20_model.r INFO @ Sun, 21 Jun 2020 18:57:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:57:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.10_summits.bed INFO @ Sun, 21 Jun 2020 18:57:57: Done! pass1 - making usageList (302 chroms): 2 millis pass2 - checking and writing primary data (7867 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618516/SRX2618516.20_summits.bed INFO @ Sun, 21 Jun 2020 18:58:23: Done! pass1 - making usageList (128 chroms): 2 millis pass2 - checking and writing primary data (6762 records, 4 fields): 11 millis CompletedMACS2peakCalling