Job ID = 6454802 SRX = SRX2592401 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:33:43 prefetch.2.10.7: 1) Downloading 'SRR5289678'... 2020-06-21T09:33:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:38 prefetch.2.10.7: 1) 'SRR5289678' was downloaded successfully Read 27805923 spots for SRR5289678/SRR5289678.sra Written 27805923 spots for SRR5289678/SRR5289678.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: 00:08:00 27805923 reads; of these: 27805923 (100.00%) were unpaired; of these: 1959318 (7.05%) aligned 0 times 20901107 (75.17%) aligned exactly 1 time 4945498 (17.79%) aligned >1 times 92.95% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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 12 files... [bam_rmdupse_core] 9089872 / 25846605 = 0.3517 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 18:55:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.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 18:55:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:28: 1000000 INFO @ Sun, 21 Jun 2020 18:55:35: 2000000 INFO @ Sun, 21 Jun 2020 18:55:42: 3000000 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 18:55:50: 4000000 INFO @ Sun, 21 Jun 2020 18:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.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 18:55:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:57: 5000000 INFO @ Sun, 21 Jun 2020 18:55:59: 1000000 INFO @ Sun, 21 Jun 2020 18:56:05: 6000000 INFO @ Sun, 21 Jun 2020 18:56:07: 2000000 INFO @ Sun, 21 Jun 2020 18:56:13: 7000000 INFO @ Sun, 21 Jun 2020 18:56:16: 3000000 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 18:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.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 18:56:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:21: 8000000 INFO @ Sun, 21 Jun 2020 18:56:24: 4000000 INFO @ Sun, 21 Jun 2020 18:56:29: 1000000 INFO @ Sun, 21 Jun 2020 18:56:30: 9000000 INFO @ Sun, 21 Jun 2020 18:56:32: 5000000 INFO @ Sun, 21 Jun 2020 18:56:38: 2000000 INFO @ Sun, 21 Jun 2020 18:56:38: 10000000 INFO @ Sun, 21 Jun 2020 18:56:40: 6000000 INFO @ Sun, 21 Jun 2020 18:56:46: 3000000 INFO @ Sun, 21 Jun 2020 18:56:46: 11000000 INFO @ Sun, 21 Jun 2020 18:56:49: 7000000 INFO @ Sun, 21 Jun 2020 18:56:54: 4000000 INFO @ Sun, 21 Jun 2020 18:56:55: 12000000 INFO @ Sun, 21 Jun 2020 18:56:57: 8000000 INFO @ Sun, 21 Jun 2020 18:57:02: 5000000 INFO @ Sun, 21 Jun 2020 18:57:03: 13000000 INFO @ Sun, 21 Jun 2020 18:57:06: 9000000 INFO @ Sun, 21 Jun 2020 18:57:11: 6000000 INFO @ Sun, 21 Jun 2020 18:57:12: 14000000 INFO @ Sun, 21 Jun 2020 18:57:14: 10000000 INFO @ Sun, 21 Jun 2020 18:57:19: 7000000 INFO @ Sun, 21 Jun 2020 18:57:20: 15000000 INFO @ Sun, 21 Jun 2020 18:57:22: 11000000 INFO @ Sun, 21 Jun 2020 18:57:27: 8000000 INFO @ Sun, 21 Jun 2020 18:57:28: 16000000 INFO @ Sun, 21 Jun 2020 18:57:31: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:57:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:57:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:57:35: #1 total tags in treatment: 16756733 INFO @ Sun, 21 Jun 2020 18:57:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:35: #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 18:57:35: #1 tags after filtering in treatment: 16756648 INFO @ Sun, 21 Jun 2020 18:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:36: 9000000 INFO @ Sun, 21 Jun 2020 18:57:37: #2 number of paired peaks: 3041 INFO @ Sun, 21 Jun 2020 18:57:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:37: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 18:57:37: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 18:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.05_model.r INFO @ Sun, 21 Jun 2020 18:57:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:40: 13000000 INFO @ Sun, 21 Jun 2020 18:57:44: 10000000 INFO @ Sun, 21 Jun 2020 18:57:48: 14000000 INFO @ Sun, 21 Jun 2020 18:57:52: 11000000 INFO @ Sun, 21 Jun 2020 18:57:57: 15000000 INFO @ Sun, 21 Jun 2020 18:58:00: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:58:05: 16000000 INFO @ Sun, 21 Jun 2020 18:58:09: 13000000 INFO @ Sun, 21 Jun 2020 18:58:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:12: #1 total tags in treatment: 16756733 INFO @ Sun, 21 Jun 2020 18:58:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:12: #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 18:58:12: #1 tags after filtering in treatment: 16756648 INFO @ Sun, 21 Jun 2020 18:58:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:14: #2 number of paired peaks: 3041 INFO @ Sun, 21 Jun 2020 18:58:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:14: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 18:58:14: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 18:58:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.10_model.r INFO @ Sun, 21 Jun 2020 18:58:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:17: 14000000 INFO @ Sun, 21 Jun 2020 18:58:24: 15000000 INFO @ Sun, 21 Jun 2020 18:58:32: 16000000 INFO @ Sun, 21 Jun 2020 18:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.05_summits.bed INFO @ Sun, 21 Jun 2020 18:58:38: Done! INFO @ Sun, 21 Jun 2020 18:58:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:38: #1 total tags in treatment: 16756733 INFO @ Sun, 21 Jun 2020 18:58:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (364 chroms): 4 millis pass2 - checking and writing primary data (20392 records, 4 fields): 28 millis INFO @ Sun, 21 Jun 2020 18:58:39: #1 tags after filtering in treatment: 16756648 INFO @ Sun, 21 Jun 2020 18:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:39: #2 looking for paired plus/minus strand peaks... CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:40: #2 number of paired peaks: 3041 INFO @ Sun, 21 Jun 2020 18:58:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:40: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 18:58:40: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 18:58:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.20_model.r INFO @ Sun, 21 Jun 2020 18:58:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.10_summits.bed INFO @ Sun, 21 Jun 2020 18:59:17: Done! pass1 - making usageList (275 chroms): 4 millis pass2 - checking and writing primary data (17112 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:59:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592401/SRX2592401.20_summits.bed INFO @ Sun, 21 Jun 2020 18:59:40: Done! pass1 - making usageList (178 chroms): 3 millis pass2 - checking and writing primary data (11818 records, 4 fields): 17 millis CompletedMACS2peakCalling