Job ID = 16439003 SRX = SRX15206441 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:23:00 prefetch.2.10.7: 1) Downloading 'SRR19139370'... 2022-08-02T05:23:00 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:23:21 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:23:22 prefetch.2.10.7: 'SRR19139370' is valid 2022-08-02T05:23:22 prefetch.2.10.7: 1) 'SRR19139370' was downloaded successfully 2022-08-02T05:23:22 prefetch.2.10.7: 'SRR19139370' has 0 unresolved dependencies Read 19624821 spots for SRR19139370/SRR19139370.sra Written 19624821 spots for SRR19139370/SRR19139370.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439149 ("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: 00:05:22 19624821 reads; of these: 19624821 (100.00%) were unpaired; of these: 1898707 (9.68%) aligned 0 times 9821050 (50.04%) aligned exactly 1 time 7905064 (40.28%) aligned >1 times 90.32% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 7763994 / 17726114 = 0.4380 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 14:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.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 14:32:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:32:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:32:52: 1000000 INFO @ Tue, 02 Aug 2022 14:32:57: 2000000 INFO @ Tue, 02 Aug 2022 14:33:02: 3000000 INFO @ Tue, 02 Aug 2022 14:33:07: 4000000 INFO @ Tue, 02 Aug 2022 14:33:12: 5000000 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 14:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.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 14:33:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:33:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:33:18: 6000000 INFO @ Tue, 02 Aug 2022 14:33:22: 1000000 INFO @ Tue, 02 Aug 2022 14:33:23: 7000000 INFO @ Tue, 02 Aug 2022 14:33:28: 2000000 INFO @ Tue, 02 Aug 2022 14:33:29: 8000000 INFO @ Tue, 02 Aug 2022 14:33:34: 3000000 INFO @ Tue, 02 Aug 2022 14:33:35: 9000000 INFO @ Tue, 02 Aug 2022 14:33:39: 4000000 INFO @ Tue, 02 Aug 2022 14:33:41: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:33:41: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:33:41: #1 total tags in treatment: 9962120 INFO @ Tue, 02 Aug 2022 14:33:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:33:41: #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 14:33:41: #1 tags after filtering in treatment: 9962120 INFO @ Tue, 02 Aug 2022 14:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:33:41: #1 finished! INFO @ Tue, 02 Aug 2022 14:33:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:33:42: #2 number of paired peaks: 3787 INFO @ Tue, 02 Aug 2022 14:33:42: start model_add_line... INFO @ Tue, 02 Aug 2022 14:33:42: start X-correlation... INFO @ Tue, 02 Aug 2022 14:33:42: end of X-cor INFO @ Tue, 02 Aug 2022 14:33:42: #2 finished! INFO @ Tue, 02 Aug 2022 14:33:42: #2 predicted fragment length is 111 bps INFO @ Tue, 02 Aug 2022 14:33:42: #2 alternative fragment length(s) may be 4,111 bps INFO @ Tue, 02 Aug 2022 14:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.05_model.r INFO @ Tue, 02 Aug 2022 14:33:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:33:42: #3 Pre-compute pvalue-qvalue table... 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 14:33:45: 5000000 INFO @ Tue, 02 Aug 2022 14:33:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.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 14:33:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:33:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:33:50: 6000000 INFO @ Tue, 02 Aug 2022 14:33:53: 1000000 INFO @ Tue, 02 Aug 2022 14:33:56: 7000000 INFO @ Tue, 02 Aug 2022 14:34:00: 2000000 INFO @ Tue, 02 Aug 2022 14:34:02: 8000000 INFO @ Tue, 02 Aug 2022 14:34:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:34:06: 3000000 INFO @ Tue, 02 Aug 2022 14:34:08: 9000000 INFO @ Tue, 02 Aug 2022 14:34:13: 4000000 INFO @ Tue, 02 Aug 2022 14:34:14: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:34:14: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:34:14: #1 total tags in treatment: 9962120 INFO @ Tue, 02 Aug 2022 14:34:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:34:14: #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 14:34:14: #1 tags after filtering in treatment: 9962120 INFO @ Tue, 02 Aug 2022 14:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:34:14: #1 finished! INFO @ Tue, 02 Aug 2022 14:34:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:34:15: #2 number of paired peaks: 3787 INFO @ Tue, 02 Aug 2022 14:34:15: start model_add_line... INFO @ Tue, 02 Aug 2022 14:34:15: start X-correlation... INFO @ Tue, 02 Aug 2022 14:34:15: end of X-cor INFO @ Tue, 02 Aug 2022 14:34:15: #2 finished! INFO @ Tue, 02 Aug 2022 14:34:15: #2 predicted fragment length is 111 bps INFO @ Tue, 02 Aug 2022 14:34:15: #2 alternative fragment length(s) may be 4,111 bps INFO @ Tue, 02 Aug 2022 14:34:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.10_model.r INFO @ Tue, 02 Aug 2022 14:34:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:34:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:34:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:34:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:34:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.05_summits.bed INFO @ Tue, 02 Aug 2022 14:34:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8115 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:34:19: 5000000 INFO @ Tue, 02 Aug 2022 14:34:25: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:34:31: 7000000 INFO @ Tue, 02 Aug 2022 14:34:37: 8000000 INFO @ Tue, 02 Aug 2022 14:34:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:34:43: 9000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:34:49: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:34:49: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:34:49: #1 total tags in treatment: 9962120 INFO @ Tue, 02 Aug 2022 14:34:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:34:49: #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 14:34:49: #1 tags after filtering in treatment: 9962120 INFO @ Tue, 02 Aug 2022 14:34:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:34:49: #1 finished! INFO @ Tue, 02 Aug 2022 14:34:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:34:50: #2 number of paired peaks: 3787 INFO @ Tue, 02 Aug 2022 14:34:50: start model_add_line... INFO @ Tue, 02 Aug 2022 14:34:50: start X-correlation... INFO @ Tue, 02 Aug 2022 14:34:50: end of X-cor INFO @ Tue, 02 Aug 2022 14:34:50: #2 finished! INFO @ Tue, 02 Aug 2022 14:34:50: #2 predicted fragment length is 111 bps INFO @ Tue, 02 Aug 2022 14:34:50: #2 alternative fragment length(s) may be 4,111 bps INFO @ Tue, 02 Aug 2022 14:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.20_model.r INFO @ Tue, 02 Aug 2022 14:34:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:34:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:34:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:34:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.10_summits.bed INFO @ Tue, 02 Aug 2022 14:34:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4609 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:35:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206441/SRX15206441.20_summits.bed INFO @ Tue, 02 Aug 2022 14:35:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2232 records, 4 fields): 78 millis CompletedMACS2peakCalling