Job ID = 12264846 SRX = SRX2745540 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21881549 spots for SRR5457477/SRR5457477.sra Written 21881549 spots for SRR5457477/SRR5457477.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265491 ("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: 00:50:41 21881549 reads; of these: 21881549 (100.00%) were paired; of these: 3322760 (15.19%) aligned concordantly 0 times 11872983 (54.26%) aligned concordantly exactly 1 time 6685806 (30.55%) aligned concordantly >1 times ---- 3322760 pairs aligned concordantly 0 times; of these: 1068670 (32.16%) aligned discordantly 1 time ---- 2254090 pairs aligned 0 times concordantly or discordantly; of these: 4508180 mates make up the pairs; of these: 2621398 (58.15%) aligned 0 times 583740 (12.95%) aligned exactly 1 time 1303042 (28.90%) aligned >1 times 94.01% overall alignment rate Time searching: 00:50:41 Overall time: 00:50:41 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 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 10111825 / 19532434 = 0.5177 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.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, 03 Apr 2021 06:56:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:56:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:56:56: 1000000 INFO @ Sat, 03 Apr 2021 06:57:04: 2000000 INFO @ Sat, 03 Apr 2021 06:57:12: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.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, 03 Apr 2021 06:57:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:57:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:57:20: 4000000 INFO @ Sat, 03 Apr 2021 06:57:26: 1000000 INFO @ Sat, 03 Apr 2021 06:57:28: 5000000 INFO @ Sat, 03 Apr 2021 06:57:35: 2000000 INFO @ Sat, 03 Apr 2021 06:57:36: 6000000 INFO @ Sat, 03 Apr 2021 06:57:43: 3000000 INFO @ Sat, 03 Apr 2021 06:57:44: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.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, 03 Apr 2021 06:57:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:57:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:57:51: 4000000 INFO @ Sat, 03 Apr 2021 06:57:52: 8000000 INFO @ Sat, 03 Apr 2021 06:57:59: 5000000 INFO @ Sat, 03 Apr 2021 06:57:59: 1000000 INFO @ Sat, 03 Apr 2021 06:58:00: 9000000 INFO @ Sat, 03 Apr 2021 06:58:07: 6000000 INFO @ Sat, 03 Apr 2021 06:58:07: 10000000 INFO @ Sat, 03 Apr 2021 06:58:11: 2000000 INFO @ Sat, 03 Apr 2021 06:58:15: 7000000 INFO @ Sat, 03 Apr 2021 06:58:15: 11000000 INFO @ Sat, 03 Apr 2021 06:58:22: 3000000 INFO @ Sat, 03 Apr 2021 06:58:23: 8000000 INFO @ Sat, 03 Apr 2021 06:58:23: 12000000 INFO @ Sat, 03 Apr 2021 06:58:31: 9000000 INFO @ Sat, 03 Apr 2021 06:58:31: 13000000 INFO @ Sat, 03 Apr 2021 06:58:33: 4000000 INFO @ Sat, 03 Apr 2021 06:58:39: 10000000 INFO @ Sat, 03 Apr 2021 06:58:40: 14000000 INFO @ Sat, 03 Apr 2021 06:58:43: 5000000 INFO @ Sat, 03 Apr 2021 06:58:47: 11000000 INFO @ Sat, 03 Apr 2021 06:58:48: 15000000 INFO @ Sat, 03 Apr 2021 06:58:53: 6000000 INFO @ Sat, 03 Apr 2021 06:58:55: 12000000 INFO @ Sat, 03 Apr 2021 06:58:57: 16000000 INFO @ Sat, 03 Apr 2021 06:59:03: 13000000 INFO @ Sat, 03 Apr 2021 06:59:03: 7000000 INFO @ Sat, 03 Apr 2021 06:59:05: 17000000 INFO @ Sat, 03 Apr 2021 06:59:12: 14000000 INFO @ Sat, 03 Apr 2021 06:59:13: 18000000 INFO @ Sat, 03 Apr 2021 06:59:13: 8000000 INFO @ Sat, 03 Apr 2021 06:59:21: 15000000 INFO @ Sat, 03 Apr 2021 06:59:21: 19000000 INFO @ Sat, 03 Apr 2021 06:59:23: 9000000 INFO @ Sat, 03 Apr 2021 06:59:29: 16000000 INFO @ Sat, 03 Apr 2021 06:59:29: 20000000 INFO @ Sat, 03 Apr 2021 06:59:33: 10000000 INFO @ Sat, 03 Apr 2021 06:59:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:59:37: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:59:37: #1 total tags in treatment: 8766836 INFO @ Sat, 03 Apr 2021 06:59:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:59:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:59:37: #1 tags after filtering in treatment: 6448554 INFO @ Sat, 03 Apr 2021 06:59:37: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:59:37: #1 finished! INFO @ Sat, 03 Apr 2021 06:59:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:59:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:59:37: 17000000 INFO @ Sat, 03 Apr 2021 06:59:38: #2 number of paired peaks: 3272 INFO @ Sat, 03 Apr 2021 06:59:38: start model_add_line... INFO @ Sat, 03 Apr 2021 06:59:38: start X-correlation... INFO @ Sat, 03 Apr 2021 06:59:38: end of X-cor INFO @ Sat, 03 Apr 2021 06:59:38: #2 finished! INFO @ Sat, 03 Apr 2021 06:59:38: #2 predicted fragment length is 120 bps INFO @ Sat, 03 Apr 2021 06:59:38: #2 alternative fragment length(s) may be 120 bps INFO @ Sat, 03 Apr 2021 06:59:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.05_model.r INFO @ Sat, 03 Apr 2021 06:59:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:59:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:59:42: 11000000 INFO @ Sat, 03 Apr 2021 06:59:45: 18000000 INFO @ Sat, 03 Apr 2021 06:59:52: 12000000 INFO @ Sat, 03 Apr 2021 06:59:53: 19000000 INFO @ Sat, 03 Apr 2021 06:59:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:00:01: 20000000 INFO @ Sat, 03 Apr 2021 07:00:02: 13000000 INFO @ Sat, 03 Apr 2021 07:00:08: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:00:08: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:00:08: #1 total tags in treatment: 8766836 INFO @ Sat, 03 Apr 2021 07:00:08: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:00:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:00:08: #1 tags after filtering in treatment: 6448554 INFO @ Sat, 03 Apr 2021 07:00:08: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:00:08: #1 finished! INFO @ Sat, 03 Apr 2021 07:00:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:00:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:00:09: #2 number of paired peaks: 3272 INFO @ Sat, 03 Apr 2021 07:00:09: start model_add_line... INFO @ Sat, 03 Apr 2021 07:00:09: start X-correlation... INFO @ Sat, 03 Apr 2021 07:00:09: end of X-cor INFO @ Sat, 03 Apr 2021 07:00:09: #2 finished! INFO @ Sat, 03 Apr 2021 07:00:09: #2 predicted fragment length is 120 bps INFO @ Sat, 03 Apr 2021 07:00:09: #2 alternative fragment length(s) may be 120 bps INFO @ Sat, 03 Apr 2021 07:00:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.10_model.r INFO @ Sat, 03 Apr 2021 07:00:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:00:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:00:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:00:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:00:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.05_summits.bed INFO @ Sat, 03 Apr 2021 07:00:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10509 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:00:13: 14000000 INFO @ Sat, 03 Apr 2021 07:00:24: 15000000 INFO @ Sat, 03 Apr 2021 07:00:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:00:34: 16000000 INFO @ Sat, 03 Apr 2021 07:00:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:00:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:00:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.10_summits.bed INFO @ Sat, 03 Apr 2021 07:00:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5869 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:00:44: 17000000 INFO @ Sat, 03 Apr 2021 07:00:54: 18000000 INFO @ Sat, 03 Apr 2021 07:01:03: 19000000 INFO @ Sat, 03 Apr 2021 07:01:13: 20000000 INFO @ Sat, 03 Apr 2021 07:01:22: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:01:22: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:01:22: #1 total tags in treatment: 8766836 INFO @ Sat, 03 Apr 2021 07:01:22: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:01:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:01:22: #1 tags after filtering in treatment: 6448554 INFO @ Sat, 03 Apr 2021 07:01:22: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:01:22: #1 finished! INFO @ Sat, 03 Apr 2021 07:01:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:01:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:01:23: #2 number of paired peaks: 3272 INFO @ Sat, 03 Apr 2021 07:01:23: start model_add_line... INFO @ Sat, 03 Apr 2021 07:01:23: start X-correlation... INFO @ Sat, 03 Apr 2021 07:01:23: end of X-cor INFO @ Sat, 03 Apr 2021 07:01:23: #2 finished! INFO @ Sat, 03 Apr 2021 07:01:23: #2 predicted fragment length is 120 bps INFO @ Sat, 03 Apr 2021 07:01:23: #2 alternative fragment length(s) may be 120 bps INFO @ Sat, 03 Apr 2021 07:01:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.20_model.r INFO @ Sat, 03 Apr 2021 07:01:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:01:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:01:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:01:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:01:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:01:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2745540/SRX2745540.20_summits.bed INFO @ Sat, 03 Apr 2021 07:01:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2640 records, 4 fields): 10 millis CompletedMACS2peakCalling