Job ID = 14172489 SRX = SRX7628896 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19315418 spots for SRR10963258/SRR10963258.sra Written 19315418 spots for SRR10963258/SRR10963258.sra fastq に変換しました。 bowtie でマッピング中... Your job 14173005 ("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: 00:20:39 19315418 reads; of these: 19315418 (100.00%) were paired; of these: 8202372 (42.47%) aligned concordantly 0 times 8144461 (42.17%) aligned concordantly exactly 1 time 2968585 (15.37%) aligned concordantly >1 times ---- 8202372 pairs aligned concordantly 0 times; of these: 55090 (0.67%) aligned discordantly 1 time ---- 8147282 pairs aligned 0 times concordantly or discordantly; of these: 16294564 mates make up the pairs; of these: 15687294 (96.27%) aligned 0 times 307837 (1.89%) aligned exactly 1 time 299433 (1.84%) aligned >1 times 59.39% overall alignment rate Time searching: 00:20:39 Overall time: 00:20:39 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 12 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] 772218 / 11163453 = 0.0692 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:05:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.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, 11 Dec 2021 16:05:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:05:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:05:16: 1000000 INFO @ Sat, 11 Dec 2021 16:05:23: 2000000 INFO @ Sat, 11 Dec 2021 16:05:29: 3000000 INFO @ Sat, 11 Dec 2021 16:05:35: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:05:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.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, 11 Dec 2021 16:05:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:05:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:05:42: 5000000 INFO @ Sat, 11 Dec 2021 16:05:47: 1000000 INFO @ Sat, 11 Dec 2021 16:05:49: 6000000 INFO @ Sat, 11 Dec 2021 16:05:54: 2000000 INFO @ Sat, 11 Dec 2021 16:05:56: 7000000 INFO @ Sat, 11 Dec 2021 16:06:01: 3000000 INFO @ Sat, 11 Dec 2021 16:06:03: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:06:08: 4000000 INFO @ Sat, 11 Dec 2021 16:06:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.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, 11 Dec 2021 16:06:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:06:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:06:10: 9000000 INFO @ Sat, 11 Dec 2021 16:06:15: 5000000 INFO @ Sat, 11 Dec 2021 16:06:17: 1000000 INFO @ Sat, 11 Dec 2021 16:06:17: 10000000 INFO @ Sat, 11 Dec 2021 16:06:23: 6000000 INFO @ Sat, 11 Dec 2021 16:06:24: 2000000 INFO @ Sat, 11 Dec 2021 16:06:25: 11000000 INFO @ Sat, 11 Dec 2021 16:06:30: 7000000 INFO @ Sat, 11 Dec 2021 16:06:31: 3000000 INFO @ Sat, 11 Dec 2021 16:06:32: 12000000 INFO @ Sat, 11 Dec 2021 16:06:37: 8000000 INFO @ Sat, 11 Dec 2021 16:06:38: 4000000 INFO @ Sat, 11 Dec 2021 16:06:39: 13000000 INFO @ Sat, 11 Dec 2021 16:06:44: 9000000 INFO @ Sat, 11 Dec 2021 16:06:45: 5000000 INFO @ Sat, 11 Dec 2021 16:06:46: 14000000 INFO @ Sat, 11 Dec 2021 16:06:51: 10000000 INFO @ Sat, 11 Dec 2021 16:06:53: 6000000 INFO @ Sat, 11 Dec 2021 16:06:54: 15000000 INFO @ Sat, 11 Dec 2021 16:06:58: 11000000 INFO @ Sat, 11 Dec 2021 16:07:00: 7000000 INFO @ Sat, 11 Dec 2021 16:07:01: 16000000 INFO @ Sat, 11 Dec 2021 16:07:05: 12000000 INFO @ Sat, 11 Dec 2021 16:07:07: 8000000 INFO @ Sat, 11 Dec 2021 16:07:08: 17000000 INFO @ Sat, 11 Dec 2021 16:07:13: 13000000 INFO @ Sat, 11 Dec 2021 16:07:15: 9000000 INFO @ Sat, 11 Dec 2021 16:07:15: 18000000 INFO @ Sat, 11 Dec 2021 16:07:20: 14000000 INFO @ Sat, 11 Dec 2021 16:07:22: 10000000 INFO @ Sat, 11 Dec 2021 16:07:22: 19000000 INFO @ Sat, 11 Dec 2021 16:07:27: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:07:29: 11000000 INFO @ Sat, 11 Dec 2021 16:07:29: 20000000 INFO @ Sat, 11 Dec 2021 16:07:34: 16000000 INFO @ Sat, 11 Dec 2021 16:07:36: 21000000 INFO @ Sat, 11 Dec 2021 16:07:36: 12000000 INFO @ Sat, 11 Dec 2021 16:07:39: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:07:39: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:07:39: #1 total tags in treatment: 10342699 INFO @ Sat, 11 Dec 2021 16:07:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:07:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:07:39: #1 tags after filtering in treatment: 8926850 INFO @ Sat, 11 Dec 2021 16:07:39: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 16:07:39: #1 finished! INFO @ Sat, 11 Dec 2021 16:07:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:07:40: #2 number of paired peaks: 5808 INFO @ Sat, 11 Dec 2021 16:07:40: start model_add_line... INFO @ Sat, 11 Dec 2021 16:07:40: start X-correlation... INFO @ Sat, 11 Dec 2021 16:07:40: end of X-cor INFO @ Sat, 11 Dec 2021 16:07:40: #2 finished! INFO @ Sat, 11 Dec 2021 16:07:40: #2 predicted fragment length is 183 bps INFO @ Sat, 11 Dec 2021 16:07:40: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 11 Dec 2021 16:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.05_model.r INFO @ Sat, 11 Dec 2021 16:07:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:07:41: 17000000 INFO @ Sat, 11 Dec 2021 16:07:44: 13000000 INFO @ Sat, 11 Dec 2021 16:07:48: 18000000 INFO @ Sat, 11 Dec 2021 16:07:51: 14000000 INFO @ Sat, 11 Dec 2021 16:07:55: 19000000 INFO @ Sat, 11 Dec 2021 16:07:58: 15000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:08:02: 20000000 INFO @ Sat, 11 Dec 2021 16:08:05: 16000000 INFO @ Sat, 11 Dec 2021 16:08:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:08:10: 21000000 INFO @ Sat, 11 Dec 2021 16:08:12: 17000000 INFO @ Sat, 11 Dec 2021 16:08:12: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:08:12: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:08:12: #1 total tags in treatment: 10342699 INFO @ Sat, 11 Dec 2021 16:08:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:08:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:08:12: #1 tags after filtering in treatment: 8926850 INFO @ Sat, 11 Dec 2021 16:08:12: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 16:08:12: #1 finished! INFO @ Sat, 11 Dec 2021 16:08:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:08:13: #2 number of paired peaks: 5808 INFO @ Sat, 11 Dec 2021 16:08:13: start model_add_line... INFO @ Sat, 11 Dec 2021 16:08:13: start X-correlation... INFO @ Sat, 11 Dec 2021 16:08:13: end of X-cor INFO @ Sat, 11 Dec 2021 16:08:13: #2 finished! INFO @ Sat, 11 Dec 2021 16:08:13: #2 predicted fragment length is 183 bps INFO @ Sat, 11 Dec 2021 16:08:13: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 11 Dec 2021 16:08:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.10_model.r INFO @ Sat, 11 Dec 2021 16:08:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:08:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:08:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:08:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:08:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.05_summits.bed INFO @ Sat, 11 Dec 2021 16:08:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9102 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:08:18: 18000000 INFO @ Sat, 11 Dec 2021 16:08:25: 19000000 INFO @ Sat, 11 Dec 2021 16:08:31: 20000000 INFO @ Sat, 11 Dec 2021 16:08:37: 21000000 INFO @ Sat, 11 Dec 2021 16:08:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:08:40: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:08:40: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:08:40: #1 total tags in treatment: 10342699 INFO @ Sat, 11 Dec 2021 16:08:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:08:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:08:40: #1 tags after filtering in treatment: 8926850 INFO @ Sat, 11 Dec 2021 16:08:40: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 16:08:40: #1 finished! INFO @ Sat, 11 Dec 2021 16:08:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:08:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:08:41: #2 number of paired peaks: 5808 INFO @ Sat, 11 Dec 2021 16:08:41: start model_add_line... INFO @ Sat, 11 Dec 2021 16:08:41: start X-correlation... INFO @ Sat, 11 Dec 2021 16:08:41: end of X-cor INFO @ Sat, 11 Dec 2021 16:08:41: #2 finished! INFO @ Sat, 11 Dec 2021 16:08:41: #2 predicted fragment length is 183 bps INFO @ Sat, 11 Dec 2021 16:08:41: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 11 Dec 2021 16:08:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.20_model.r INFO @ Sat, 11 Dec 2021 16:08:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:08:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.10_summits.bed INFO @ Sat, 11 Dec 2021 16:08:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6282 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:09:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:09:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:09:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:09:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628896/SRX7628896.20_summits.bed INFO @ Sat, 11 Dec 2021 16:09:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3559 records, 4 fields): 5 millis CompletedMACS2peakCalling