Job ID = 6454616 SRX = SRX2399659 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:22:44 prefetch.2.10.7: 1) Downloading 'SRR5081493'... 2020-06-21T09:22:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:26:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:26:24 prefetch.2.10.7: 1) 'SRR5081493' was downloaded successfully 2020-06-21T09:26:24 prefetch.2.10.7: 'SRR5081493' has 0 unresolved dependencies Read 25579468 spots for SRR5081493/SRR5081493.sra Written 25579468 spots for SRR5081493/SRR5081493.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: 00:07:26 25579468 reads; of these: 25579468 (100.00%) were unpaired; of these: 4596640 (17.97%) aligned 0 times 12757834 (49.88%) aligned exactly 1 time 8224994 (32.15%) aligned >1 times 82.03% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 7049375 / 20982828 = 0.3360 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 18:39:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.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 18:39:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:08: 1000000 INFO @ Sun, 21 Jun 2020 18:40:22: 2000000 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 18:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.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 18:40:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:29: 3000000 INFO @ Sun, 21 Jun 2020 18:40:33: 1000000 INFO @ Sun, 21 Jun 2020 18:40:36: 4000000 INFO @ Sun, 21 Jun 2020 18:40:40: 2000000 INFO @ Sun, 21 Jun 2020 18:40:44: 5000000 INFO @ Sun, 21 Jun 2020 18:40:48: 3000000 INFO @ Sun, 21 Jun 2020 18:40:51: 6000000 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 18:40:55: 4000000 INFO @ Sun, 21 Jun 2020 18:40:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.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 18:40:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:59: 7000000 INFO @ Sun, 21 Jun 2020 18:41:02: 5000000 INFO @ Sun, 21 Jun 2020 18:41:02: 1000000 INFO @ Sun, 21 Jun 2020 18:41:07: 8000000 INFO @ Sun, 21 Jun 2020 18:41:09: 2000000 INFO @ Sun, 21 Jun 2020 18:41:10: 6000000 INFO @ Sun, 21 Jun 2020 18:41:14: 9000000 INFO @ Sun, 21 Jun 2020 18:41:16: 3000000 INFO @ Sun, 21 Jun 2020 18:41:18: 7000000 INFO @ Sun, 21 Jun 2020 18:41:21: 10000000 INFO @ Sun, 21 Jun 2020 18:41:23: 4000000 INFO @ Sun, 21 Jun 2020 18:41:25: 8000000 INFO @ Sun, 21 Jun 2020 18:41:29: 11000000 INFO @ Sun, 21 Jun 2020 18:41:30: 5000000 INFO @ Sun, 21 Jun 2020 18:41:33: 9000000 INFO @ Sun, 21 Jun 2020 18:41:37: 6000000 INFO @ Sun, 21 Jun 2020 18:41:37: 12000000 INFO @ Sun, 21 Jun 2020 18:41:40: 10000000 INFO @ Sun, 21 Jun 2020 18:41:44: 7000000 INFO @ Sun, 21 Jun 2020 18:41:44: 13000000 INFO @ Sun, 21 Jun 2020 18:41:48: 11000000 INFO @ Sun, 21 Jun 2020 18:41:50: 8000000 INFO @ Sun, 21 Jun 2020 18:41:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:41:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:41:51: #1 total tags in treatment: 13933453 INFO @ Sun, 21 Jun 2020 18:41:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:51: #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 18:41:52: #1 tags after filtering in treatment: 13933452 INFO @ Sun, 21 Jun 2020 18:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:53: #2 number of paired peaks: 7498 INFO @ Sun, 21 Jun 2020 18:41:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:53: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 18:41:53: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 21 Jun 2020 18:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.05_model.r INFO @ Sun, 21 Jun 2020 18:41:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:41:55: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:41:57: 9000000 INFO @ Sun, 21 Jun 2020 18:42:03: 13000000 INFO @ Sun, 21 Jun 2020 18:42:04: 10000000 INFO @ Sun, 21 Jun 2020 18:42:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:42:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:42:10: #1 total tags in treatment: 13933453 INFO @ Sun, 21 Jun 2020 18:42:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:42:10: #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 18:42:10: #1 tags after filtering in treatment: 13933452 INFO @ Sun, 21 Jun 2020 18:42:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:42:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:42:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:42:11: 11000000 INFO @ Sun, 21 Jun 2020 18:42:12: #2 number of paired peaks: 7498 INFO @ Sun, 21 Jun 2020 18:42:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:42:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:42:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:42:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:42:12: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 18:42:12: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 21 Jun 2020 18:42:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.10_model.r INFO @ Sun, 21 Jun 2020 18:42:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:42:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:42:17: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:42:22: 13000000 INFO @ Sun, 21 Jun 2020 18:42:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:42:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:42:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:42:28: #1 total tags in treatment: 13933453 INFO @ Sun, 21 Jun 2020 18:42:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:42:28: #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 18:42:28: #1 tags after filtering in treatment: 13933452 INFO @ Sun, 21 Jun 2020 18:42:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:42:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:42:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:42:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:42:30: #2 number of paired peaks: 7498 INFO @ Sun, 21 Jun 2020 18:42:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:42:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:42:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:42:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:42:30: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 18:42:30: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 21 Jun 2020 18:42:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.20_model.r INFO @ Sun, 21 Jun 2020 18:42:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:42:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:42:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:42:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:42:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.05_summits.bed INFO @ Sun, 21 Jun 2020 18:42:42: Done! pass1 - making usageList (1001 chroms): 3 millis pass2 - checking and writing primary data (12701 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:42:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.10_summits.bed INFO @ Sun, 21 Jun 2020 18:43:01: Done! INFO @ Sun, 21 Jun 2020 18:43:03: #3 Call peaks for each chromosome... pass1 - making usageList (790 chroms): 2 millis pass2 - checking and writing primary data (9794 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399659/SRX2399659.20_summits.bed INFO @ Sun, 21 Jun 2020 18:43:18: Done! pass1 - making usageList (506 chroms): 2 millis pass2 - checking and writing primary data (7404 records, 4 fields): 20 millis CompletedMACS2peakCalling