Job ID = 16439753 SRX = SRX14894242 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T07:06:40 prefetch.2.10.7: 1) Downloading 'SRR18795779'... 2022-08-02T07:06:40 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T07:07:47 prefetch.2.10.7: HTTPS download succeed 2022-08-02T07:07:47 prefetch.2.10.7: 1) 'SRR18795779' was downloaded successfully 2022-08-02T07:07:47 prefetch.2.10.7: 'SRR18795779' has 0 unresolved dependencies Read 45229310 spots for SRR18795779/SRR18795779.sra Written 45229310 spots for SRR18795779/SRR18795779.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439863 ("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: 00:10:17 45229310 reads; of these: 45229310 (100.00%) were unpaired; of these: 15907200 (35.17%) aligned 0 times 24045409 (53.16%) aligned exactly 1 time 5276701 (11.67%) aligned >1 times 64.83% overall alignment rate Time searching: 00:10:18 Overall time: 00:10:18 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_rmdupse_core] 14463814 / 29322110 = 0.4933 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:26:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.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 @ Tue, 02 Aug 2022 16:26:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:26:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:26:26: 1000000 INFO @ Tue, 02 Aug 2022 16:26:33: 2000000 INFO @ Tue, 02 Aug 2022 16:26:39: 3000000 INFO @ Tue, 02 Aug 2022 16:26:44: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:26:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.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 @ Tue, 02 Aug 2022 16:26:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:26:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:26:51: 5000000 INFO @ Tue, 02 Aug 2022 16:26:57: 1000000 INFO @ Tue, 02 Aug 2022 16:26:58: 6000000 INFO @ Tue, 02 Aug 2022 16:27:04: 2000000 INFO @ Tue, 02 Aug 2022 16:27:05: 7000000 INFO @ Tue, 02 Aug 2022 16:27:11: 3000000 INFO @ Tue, 02 Aug 2022 16:27:12: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:27:18: 4000000 INFO @ Tue, 02 Aug 2022 16:27:19: 9000000 INFO @ Tue, 02 Aug 2022 16:27:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.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 @ Tue, 02 Aug 2022 16:27:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:27:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:27:25: 5000000 INFO @ Tue, 02 Aug 2022 16:27:26: 10000000 INFO @ Tue, 02 Aug 2022 16:27:27: 1000000 INFO @ Tue, 02 Aug 2022 16:27:33: 6000000 INFO @ Tue, 02 Aug 2022 16:27:34: 11000000 INFO @ Tue, 02 Aug 2022 16:27:35: 2000000 INFO @ Tue, 02 Aug 2022 16:27:40: 7000000 INFO @ Tue, 02 Aug 2022 16:27:41: 12000000 INFO @ Tue, 02 Aug 2022 16:27:42: 3000000 INFO @ Tue, 02 Aug 2022 16:27:47: 8000000 INFO @ Tue, 02 Aug 2022 16:27:48: 13000000 INFO @ Tue, 02 Aug 2022 16:27:50: 4000000 INFO @ Tue, 02 Aug 2022 16:27:55: 9000000 INFO @ Tue, 02 Aug 2022 16:27:56: 14000000 INFO @ Tue, 02 Aug 2022 16:27:57: 5000000 INFO @ Tue, 02 Aug 2022 16:28:02: 10000000 INFO @ Tue, 02 Aug 2022 16:28:02: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:28:02: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:28:02: #1 total tags in treatment: 14858296 INFO @ Tue, 02 Aug 2022 16:28:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:28:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:28:02: #1 tags after filtering in treatment: 14858296 INFO @ Tue, 02 Aug 2022 16:28:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:28:02: #1 finished! INFO @ Tue, 02 Aug 2022 16:28:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:28:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:28:04: #2 number of paired peaks: 3479 INFO @ Tue, 02 Aug 2022 16:28:04: start model_add_line... INFO @ Tue, 02 Aug 2022 16:28:04: start X-correlation... INFO @ Tue, 02 Aug 2022 16:28:04: end of X-cor INFO @ Tue, 02 Aug 2022 16:28:04: #2 finished! INFO @ Tue, 02 Aug 2022 16:28:04: #2 predicted fragment length is 245 bps INFO @ Tue, 02 Aug 2022 16:28:04: #2 alternative fragment length(s) may be 245 bps INFO @ Tue, 02 Aug 2022 16:28:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.05_model.r INFO @ Tue, 02 Aug 2022 16:28:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:28:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:28:05: 6000000 INFO @ Tue, 02 Aug 2022 16:28:09: 11000000 INFO @ Tue, 02 Aug 2022 16:28:12: 7000000 INFO @ Tue, 02 Aug 2022 16:28:16: 12000000 INFO @ Tue, 02 Aug 2022 16:28:19: 8000000 INFO @ Tue, 02 Aug 2022 16:28:23: 13000000 INFO @ Tue, 02 Aug 2022 16:28:26: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:28:30: 14000000 INFO @ Tue, 02 Aug 2022 16:28:33: 10000000 INFO @ Tue, 02 Aug 2022 16:28:36: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:28:36: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:28:36: #1 total tags in treatment: 14858296 INFO @ Tue, 02 Aug 2022 16:28:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:28:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:28:36: #1 tags after filtering in treatment: 14858296 INFO @ Tue, 02 Aug 2022 16:28:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:28:36: #1 finished! INFO @ Tue, 02 Aug 2022 16:28:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:28:38: #2 number of paired peaks: 3479 INFO @ Tue, 02 Aug 2022 16:28:38: start model_add_line... INFO @ Tue, 02 Aug 2022 16:28:38: start X-correlation... INFO @ Tue, 02 Aug 2022 16:28:38: end of X-cor INFO @ Tue, 02 Aug 2022 16:28:38: #2 finished! INFO @ Tue, 02 Aug 2022 16:28:38: #2 predicted fragment length is 245 bps INFO @ Tue, 02 Aug 2022 16:28:38: #2 alternative fragment length(s) may be 245 bps INFO @ Tue, 02 Aug 2022 16:28:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.10_model.r INFO @ Tue, 02 Aug 2022 16:28:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:28:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:28:39: 11000000 INFO @ Tue, 02 Aug 2022 16:28:46: 12000000 INFO @ Tue, 02 Aug 2022 16:28:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:28:52: 13000000 INFO @ Tue, 02 Aug 2022 16:28:58: 14000000 INFO @ Tue, 02 Aug 2022 16:29:03: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:29:03: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:29:03: #1 total tags in treatment: 14858296 INFO @ Tue, 02 Aug 2022 16:29:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:29:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:29:04: #1 tags after filtering in treatment: 14858296 INFO @ Tue, 02 Aug 2022 16:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:29:04: #1 finished! INFO @ Tue, 02 Aug 2022 16:29:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:29:04: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:29:05: #2 number of paired peaks: 3479 INFO @ Tue, 02 Aug 2022 16:29:05: start model_add_line... INFO @ Tue, 02 Aug 2022 16:29:05: start X-correlation... INFO @ Tue, 02 Aug 2022 16:29:05: end of X-cor INFO @ Tue, 02 Aug 2022 16:29:05: #2 finished! INFO @ Tue, 02 Aug 2022 16:29:05: #2 predicted fragment length is 245 bps INFO @ Tue, 02 Aug 2022 16:29:05: #2 alternative fragment length(s) may be 245 bps INFO @ Tue, 02 Aug 2022 16:29:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.20_model.r INFO @ Tue, 02 Aug 2022 16:29:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:29:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:29:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:29:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:29:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.05_summits.bed INFO @ Tue, 02 Aug 2022 16:29:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (10515 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:29:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:29:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:29:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:29:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.10_summits.bed INFO @ Tue, 02 Aug 2022 16:29:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8635 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:29:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:30:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:30:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:30:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894242/SRX14894242.20_summits.bed INFO @ Tue, 02 Aug 2022 16:30:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6610 records, 4 fields): 187 millis CompletedMACS2peakCalling