Job ID = 14172287 SRX = SRX3293003 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20146663 spots for SRR6182829/SRR6182829.sra Written 20146663 spots for SRR6182829/SRR6182829.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172782 ("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: 00:07:20 20146663 reads; of these: 20146663 (100.00%) were unpaired; of these: 831111 (4.13%) aligned 0 times 17919961 (88.95%) aligned exactly 1 time 1395591 (6.93%) aligned >1 times 95.87% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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 8 files... [bam_rmdupse_core] 8562845 / 19315552 = 0.4433 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 15:15:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.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 15:15:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:15:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:15:53: 1000000 INFO @ Sat, 11 Dec 2021 15:15:59: 2000000 INFO @ Sat, 11 Dec 2021 15:16:05: 3000000 INFO @ Sat, 11 Dec 2021 15:16:11: 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 15:16:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.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 15:16:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:16:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:16:18: 5000000 INFO @ Sat, 11 Dec 2021 15:16:24: 1000000 INFO @ Sat, 11 Dec 2021 15:16:24: 6000000 INFO @ Sat, 11 Dec 2021 15:16:30: 2000000 INFO @ Sat, 11 Dec 2021 15:16:31: 7000000 INFO @ Sat, 11 Dec 2021 15:16:37: 3000000 INFO @ Sat, 11 Dec 2021 15:16:38: 8000000 INFO @ Sat, 11 Dec 2021 15:16:44: 4000000 INFO @ Sat, 11 Dec 2021 15:16:45: 9000000 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 15:16:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.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 15:16:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:16:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:16:51: 5000000 INFO @ Sat, 11 Dec 2021 15:16:52: 10000000 INFO @ Sat, 11 Dec 2021 15:16:54: 1000000 INFO @ Sat, 11 Dec 2021 15:16:57: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:16:57: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:16:57: #1 total tags in treatment: 10752707 INFO @ Sat, 11 Dec 2021 15:16:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:16:57: #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 15:16:57: #1 tags after filtering in treatment: 10752707 INFO @ Sat, 11 Dec 2021 15:16:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:16:57: #1 finished! INFO @ Sat, 11 Dec 2021 15:16:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:16:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:16:57: 6000000 INFO @ Sat, 11 Dec 2021 15:16:58: #2 number of paired peaks: 9943 INFO @ Sat, 11 Dec 2021 15:16:58: start model_add_line... INFO @ Sat, 11 Dec 2021 15:16:58: start X-correlation... INFO @ Sat, 11 Dec 2021 15:16:58: end of X-cor INFO @ Sat, 11 Dec 2021 15:16:58: #2 finished! INFO @ Sat, 11 Dec 2021 15:16:58: #2 predicted fragment length is 295 bps INFO @ Sat, 11 Dec 2021 15:16:58: #2 alternative fragment length(s) may be 295 bps INFO @ Sat, 11 Dec 2021 15:16:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.05_model.r INFO @ Sat, 11 Dec 2021 15:16:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:16:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:17:00: 2000000 INFO @ Sat, 11 Dec 2021 15:17:04: 7000000 INFO @ Sat, 11 Dec 2021 15:17:07: 3000000 INFO @ Sat, 11 Dec 2021 15:17:11: 8000000 INFO @ Sat, 11 Dec 2021 15:17:14: 4000000 INFO @ Sat, 11 Dec 2021 15:17:18: 9000000 INFO @ Sat, 11 Dec 2021 15:17:21: 5000000 INFO @ Sat, 11 Dec 2021 15:17:24: 10000000 INFO @ Sat, 11 Dec 2021 15:17:27: 6000000 INFO @ Sat, 11 Dec 2021 15:17:29: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:17:29: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:17:29: #1 total tags in treatment: 10752707 INFO @ Sat, 11 Dec 2021 15:17:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:17:29: #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 15:17:30: #1 tags after filtering in treatment: 10752707 INFO @ Sat, 11 Dec 2021 15:17:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:17:30: #1 finished! INFO @ Sat, 11 Dec 2021 15:17:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:17:31: #2 number of paired peaks: 9943 INFO @ Sat, 11 Dec 2021 15:17:31: start model_add_line... INFO @ Sat, 11 Dec 2021 15:17:31: start X-correlation... INFO @ Sat, 11 Dec 2021 15:17:31: end of X-cor INFO @ Sat, 11 Dec 2021 15:17:31: #2 finished! INFO @ Sat, 11 Dec 2021 15:17:31: #2 predicted fragment length is 295 bps INFO @ Sat, 11 Dec 2021 15:17:31: #2 alternative fragment length(s) may be 295 bps INFO @ Sat, 11 Dec 2021 15:17:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.10_model.r INFO @ Sat, 11 Dec 2021 15:17:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:17:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:17:34: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:17:40: 8000000 INFO @ Sat, 11 Dec 2021 15:17:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:17:47: 9000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:17:53: 10000000 INFO @ Sat, 11 Dec 2021 15:17:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:17:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:17:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.05_summits.bed INFO @ Sat, 11 Dec 2021 15:17:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9348 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:17:58: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:17:58: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:17:58: #1 total tags in treatment: 10752707 INFO @ Sat, 11 Dec 2021 15:17:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:17:58: #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 15:17:58: #1 tags after filtering in treatment: 10752707 INFO @ Sat, 11 Dec 2021 15:17:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:17:58: #1 finished! INFO @ Sat, 11 Dec 2021 15:17:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:17:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:18:00: #2 number of paired peaks: 9943 INFO @ Sat, 11 Dec 2021 15:18:00: start model_add_line... INFO @ Sat, 11 Dec 2021 15:18:00: start X-correlation... INFO @ Sat, 11 Dec 2021 15:18:00: end of X-cor INFO @ Sat, 11 Dec 2021 15:18:00: #2 finished! INFO @ Sat, 11 Dec 2021 15:18:00: #2 predicted fragment length is 295 bps INFO @ Sat, 11 Dec 2021 15:18:00: #2 alternative fragment length(s) may be 295 bps INFO @ Sat, 11 Dec 2021 15:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.20_model.r INFO @ Sat, 11 Dec 2021 15:18:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:18:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:18:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.10_summits.bed INFO @ Sat, 11 Dec 2021 15:18:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7764 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:18:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:18:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:18:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:18:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3293003/SRX3293003.20_summits.bed INFO @ Sat, 11 Dec 2021 15:18:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6292 records, 4 fields): 8 millis CompletedMACS2peakCalling