Job ID = 16439756 SRX = SRX14894245 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T07:06:55 prefetch.2.10.7: 1) Downloading 'SRR18795776'... 2022-08-02T07:06:55 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T07:07:57 prefetch.2.10.7: HTTPS download succeed 2022-08-02T07:07:57 prefetch.2.10.7: 1) 'SRR18795776' was downloaded successfully 2022-08-02T07:07:57 prefetch.2.10.7: 'SRR18795776' has 0 unresolved dependencies Read 53363752 spots for SRR18795776/SRR18795776.sra Written 53363752 spots for SRR18795776/SRR18795776.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439854 ("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 53363752 reads; of these: 53363752 (100.00%) were unpaired; of these: 35990772 (67.44%) aligned 0 times 12934574 (24.24%) aligned exactly 1 time 4438406 (8.32%) aligned >1 times 32.56% 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] 10331673 / 17372980 = 0.5947 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 16:21:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.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 16:21:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:21:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:21:14: 1000000 INFO @ Tue, 02 Aug 2022 16:21:20: 2000000 INFO @ Tue, 02 Aug 2022 16:21:25: 3000000 INFO @ Tue, 02 Aug 2022 16:21:30: 4000000 INFO @ Tue, 02 Aug 2022 16:21:35: 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 16:21:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.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 16:21:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:21:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:21:41: 6000000 INFO @ Tue, 02 Aug 2022 16:21:44: 1000000 INFO @ Tue, 02 Aug 2022 16:21:46: 7000000 INFO @ Tue, 02 Aug 2022 16:21:46: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:21:46: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:21:46: #1 total tags in treatment: 7041307 INFO @ Tue, 02 Aug 2022 16:21:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:21:46: #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 16:21:46: #1 tags after filtering in treatment: 7041307 INFO @ Tue, 02 Aug 2022 16:21:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:21:46: #1 finished! INFO @ Tue, 02 Aug 2022 16:21:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:21:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:21:47: #2 number of paired peaks: 1335 INFO @ Tue, 02 Aug 2022 16:21:47: start model_add_line... INFO @ Tue, 02 Aug 2022 16:21:47: start X-correlation... INFO @ Tue, 02 Aug 2022 16:21:47: end of X-cor INFO @ Tue, 02 Aug 2022 16:21:47: #2 finished! INFO @ Tue, 02 Aug 2022 16:21:47: #2 predicted fragment length is 107 bps INFO @ Tue, 02 Aug 2022 16:21:47: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 02 Aug 2022 16:21:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.05_model.r INFO @ Tue, 02 Aug 2022 16:21:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:21:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:21:49: 2000000 INFO @ Tue, 02 Aug 2022 16:21:54: 3000000 INFO @ Tue, 02 Aug 2022 16:21:58: 4000000 INFO @ Tue, 02 Aug 2022 16:22:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:22:03: 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 16:22:07: 6000000 INFO @ Tue, 02 Aug 2022 16:22:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.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 16:22:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:22:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:22:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:22:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:22:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.05_summits.bed INFO @ Tue, 02 Aug 2022 16:22:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3311 records, 4 fields): 75 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:22:16: 7000000 INFO @ Tue, 02 Aug 2022 16:22:16: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:22:16: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:22:16: #1 total tags in treatment: 7041307 INFO @ Tue, 02 Aug 2022 16:22:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:22:16: #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 16:22:16: #1 tags after filtering in treatment: 7041307 INFO @ Tue, 02 Aug 2022 16:22:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:22:16: #1 finished! INFO @ Tue, 02 Aug 2022 16:22:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:22:16: #2 number of paired peaks: 1335 INFO @ Tue, 02 Aug 2022 16:22:16: start model_add_line... INFO @ Tue, 02 Aug 2022 16:22:17: start X-correlation... INFO @ Tue, 02 Aug 2022 16:22:17: end of X-cor INFO @ Tue, 02 Aug 2022 16:22:17: #2 finished! INFO @ Tue, 02 Aug 2022 16:22:17: #2 predicted fragment length is 107 bps INFO @ Tue, 02 Aug 2022 16:22:17: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 02 Aug 2022 16:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.10_model.r INFO @ Tue, 02 Aug 2022 16:22:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:22:18: 1000000 INFO @ Tue, 02 Aug 2022 16:22:23: 2000000 INFO @ Tue, 02 Aug 2022 16:22:27: 3000000 INFO @ Tue, 02 Aug 2022 16:22:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:22:32: 4000000 INFO @ Tue, 02 Aug 2022 16:22:37: 5000000 INFO @ Tue, 02 Aug 2022 16:22:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:22:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:22:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.10_summits.bed INFO @ Tue, 02 Aug 2022 16:22:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1769 records, 4 fields): 45 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:22:41: 6000000 INFO @ Tue, 02 Aug 2022 16:22:46: 7000000 INFO @ Tue, 02 Aug 2022 16:22:46: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:22:46: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:22:46: #1 total tags in treatment: 7041307 INFO @ Tue, 02 Aug 2022 16:22:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:22:46: #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 16:22:46: #1 tags after filtering in treatment: 7041307 INFO @ Tue, 02 Aug 2022 16:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:22:46: #1 finished! INFO @ Tue, 02 Aug 2022 16:22:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:22:47: #2 number of paired peaks: 1335 INFO @ Tue, 02 Aug 2022 16:22:47: start model_add_line... INFO @ Tue, 02 Aug 2022 16:22:47: start X-correlation... INFO @ Tue, 02 Aug 2022 16:22:47: end of X-cor INFO @ Tue, 02 Aug 2022 16:22:47: #2 finished! INFO @ Tue, 02 Aug 2022 16:22:47: #2 predicted fragment length is 107 bps INFO @ Tue, 02 Aug 2022 16:22:47: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 02 Aug 2022 16:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.20_model.r INFO @ Tue, 02 Aug 2022 16:22:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:22:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:23:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:23:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:23:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:23:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894245/SRX14894245.20_summits.bed INFO @ Tue, 02 Aug 2022 16:23:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (833 records, 4 fields): 62 millis CompletedMACS2peakCalling