Job ID = 16439751 SRX = SRX14894240 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T07:05:51 prefetch.2.10.7: 1) Downloading 'SRR18795781'... 2022-08-02T07:05:51 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T07:08:56 prefetch.2.10.7: HTTPS download succeed 2022-08-02T07:08:56 prefetch.2.10.7: 1) 'SRR18795781' was downloaded successfully 2022-08-02T07:08:56 prefetch.2.10.7: 'SRR18795781' has 0 unresolved dependencies Read 62831344 spots for SRR18795781/SRR18795781.sra Written 62831344 spots for SRR18795781/SRR18795781.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440000 ("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: 00:14:59 62831344 reads; of these: 62831344 (100.00%) were unpaired; of these: 42110722 (67.02%) aligned 0 times 16566574 (26.37%) aligned exactly 1 time 4154048 (6.61%) aligned >1 times 32.98% overall alignment rate Time searching: 00:14:59 Overall time: 00:14:59 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] 10986241 / 20720622 = 0.5302 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 16:36:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.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 16:36:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:36:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:36:31: 1000000 INFO @ Tue, 02 Aug 2022 16:36:41: 2000000 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 16:36:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.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 16:36:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:36:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:36:51: 3000000 INFO @ Tue, 02 Aug 2022 16:37:02: 1000000 INFO @ Tue, 02 Aug 2022 16:37:02: 4000000 INFO @ Tue, 02 Aug 2022 16:37:12: 2000000 INFO @ Tue, 02 Aug 2022 16:37:12: 5000000 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 16:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.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 16:37:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:37:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:37:21: 3000000 INFO @ Tue, 02 Aug 2022 16:37:22: 6000000 INFO @ Tue, 02 Aug 2022 16:37:31: 1000000 INFO @ Tue, 02 Aug 2022 16:37:31: 4000000 INFO @ Tue, 02 Aug 2022 16:37:32: 7000000 INFO @ Tue, 02 Aug 2022 16:37:41: 2000000 INFO @ Tue, 02 Aug 2022 16:37:41: 5000000 INFO @ Tue, 02 Aug 2022 16:37:42: 8000000 INFO @ Tue, 02 Aug 2022 16:37:51: 3000000 INFO @ Tue, 02 Aug 2022 16:37:51: 6000000 INFO @ Tue, 02 Aug 2022 16:37:52: 9000000 INFO @ Tue, 02 Aug 2022 16:38:00: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:38:00: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:38:00: #1 total tags in treatment: 9734381 INFO @ Tue, 02 Aug 2022 16:38:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:38:00: #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 16:38:00: #1 tags after filtering in treatment: 9734381 INFO @ Tue, 02 Aug 2022 16:38:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:38:00: #1 finished! INFO @ Tue, 02 Aug 2022 16:38:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:38:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:38:01: 7000000 INFO @ Tue, 02 Aug 2022 16:38:01: 4000000 INFO @ Tue, 02 Aug 2022 16:38:01: #2 number of paired peaks: 3320 INFO @ Tue, 02 Aug 2022 16:38:01: start model_add_line... INFO @ Tue, 02 Aug 2022 16:38:01: start X-correlation... INFO @ Tue, 02 Aug 2022 16:38:01: end of X-cor INFO @ Tue, 02 Aug 2022 16:38:01: #2 finished! INFO @ Tue, 02 Aug 2022 16:38:01: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 16:38:01: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 16:38:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.05_model.r INFO @ Tue, 02 Aug 2022 16:38:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:38:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:38:10: 5000000 INFO @ Tue, 02 Aug 2022 16:38:11: 8000000 INFO @ Tue, 02 Aug 2022 16:38:19: 6000000 INFO @ Tue, 02 Aug 2022 16:38:20: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:38:27: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:38:27: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:38:27: #1 total tags in treatment: 9734381 INFO @ Tue, 02 Aug 2022 16:38:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:38:27: #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 16:38:27: #1 tags after filtering in treatment: 9734381 INFO @ Tue, 02 Aug 2022 16:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:38:27: #1 finished! INFO @ Tue, 02 Aug 2022 16:38:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:38:28: 7000000 INFO @ Tue, 02 Aug 2022 16:38:29: #2 number of paired peaks: 3320 INFO @ Tue, 02 Aug 2022 16:38:29: start model_add_line... INFO @ Tue, 02 Aug 2022 16:38:29: start X-correlation... INFO @ Tue, 02 Aug 2022 16:38:29: end of X-cor INFO @ Tue, 02 Aug 2022 16:38:29: #2 finished! INFO @ Tue, 02 Aug 2022 16:38:29: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 16:38:29: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 16:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.10_model.r INFO @ Tue, 02 Aug 2022 16:38:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:38:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:38:37: 8000000 INFO @ Tue, 02 Aug 2022 16:38:46: 9000000 INFO @ Tue, 02 Aug 2022 16:38:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:38:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.05_summits.bed INFO @ Tue, 02 Aug 2022 16:38:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6255 records, 4 fields): 30 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:38:53: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:38:53: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:38:53: #1 total tags in treatment: 9734381 INFO @ Tue, 02 Aug 2022 16:38:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:38:53: #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 16:38:54: #1 tags after filtering in treatment: 9734381 INFO @ Tue, 02 Aug 2022 16:38:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:38:54: #1 finished! INFO @ Tue, 02 Aug 2022 16:38:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:38:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:38:55: #2 number of paired peaks: 3320 INFO @ Tue, 02 Aug 2022 16:38:55: start model_add_line... INFO @ Tue, 02 Aug 2022 16:38:55: start X-correlation... INFO @ Tue, 02 Aug 2022 16:38:55: end of X-cor INFO @ Tue, 02 Aug 2022 16:38:55: #2 finished! INFO @ Tue, 02 Aug 2022 16:38:55: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 16:38:55: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 16:38:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.20_model.r INFO @ Tue, 02 Aug 2022 16:38:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:39:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:39:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:39:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:39:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.10_summits.bed INFO @ Tue, 02 Aug 2022 16:39:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5013 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:39:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:39:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:39:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:39:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894240/SRX14894240.20_summits.bed INFO @ Tue, 02 Aug 2022 16:39:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3926 records, 4 fields): 41 millis CompletedMACS2peakCalling