Job ID = 16437582 SRX = ERX5847876 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T03:47:36 prefetch.2.10.7: 1) Downloading 'ERR6212886'... 2022-08-02T03:47:36 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T03:48:29 prefetch.2.10.7: HTTPS download succeed 2022-08-02T03:48:29 prefetch.2.10.7: 1) 'ERR6212886' was downloaded successfully 2022-08-02T03:48:29 prefetch.2.10.7: 'ERR6212886' has 0 unresolved dependencies Read 16366286 spots for ERR6212886/ERR6212886.sra Written 16366286 spots for ERR6212886/ERR6212886.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437791 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:33 16366286 reads; of these: 16366286 (100.00%) were paired; of these: 1406674 (8.59%) aligned concordantly 0 times 14396063 (87.96%) aligned concordantly exactly 1 time 563549 (3.44%) aligned concordantly >1 times ---- 1406674 pairs aligned concordantly 0 times; of these: 103428 (7.35%) aligned discordantly 1 time ---- 1303246 pairs aligned 0 times concordantly or discordantly; of these: 2606492 mates make up the pairs; of these: 1939891 (74.43%) aligned 0 times 606471 (23.27%) aligned exactly 1 time 60130 (2.31%) aligned >1 times 94.07% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 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 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 382107 / 15060190 = 0.0254 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 13:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.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 13:07:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:07:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:07:17: 1000000 INFO @ Tue, 02 Aug 2022 13:07:23: 2000000 INFO @ Tue, 02 Aug 2022 13:07:30: 3000000 INFO @ Tue, 02 Aug 2022 13:07:37: 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 13:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.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 13:07:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:07:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:07:43: 5000000 INFO @ Tue, 02 Aug 2022 13:07:47: 1000000 INFO @ Tue, 02 Aug 2022 13:07:51: 6000000 INFO @ Tue, 02 Aug 2022 13:07:54: 2000000 INFO @ Tue, 02 Aug 2022 13:07:58: 7000000 INFO @ Tue, 02 Aug 2022 13:08:02: 3000000 INFO @ Tue, 02 Aug 2022 13:08:06: 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 13:08:09: 4000000 INFO @ Tue, 02 Aug 2022 13:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.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 13:08:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:08:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:08:13: 9000000 INFO @ Tue, 02 Aug 2022 13:08:16: 5000000 INFO @ Tue, 02 Aug 2022 13:08:17: 1000000 INFO @ Tue, 02 Aug 2022 13:08:21: 10000000 INFO @ Tue, 02 Aug 2022 13:08:24: 6000000 INFO @ Tue, 02 Aug 2022 13:08:24: 2000000 INFO @ Tue, 02 Aug 2022 13:08:28: 11000000 INFO @ Tue, 02 Aug 2022 13:08:31: 7000000 INFO @ Tue, 02 Aug 2022 13:08:32: 3000000 INFO @ Tue, 02 Aug 2022 13:08:35: 12000000 INFO @ Tue, 02 Aug 2022 13:08:37: 8000000 INFO @ Tue, 02 Aug 2022 13:08:39: 4000000 INFO @ Tue, 02 Aug 2022 13:08:42: 13000000 INFO @ Tue, 02 Aug 2022 13:08:44: 9000000 INFO @ Tue, 02 Aug 2022 13:08:46: 5000000 INFO @ Tue, 02 Aug 2022 13:08:49: 14000000 INFO @ Tue, 02 Aug 2022 13:08:51: 10000000 INFO @ Tue, 02 Aug 2022 13:08:53: 6000000 INFO @ Tue, 02 Aug 2022 13:08:56: 15000000 INFO @ Tue, 02 Aug 2022 13:08:58: 11000000 INFO @ Tue, 02 Aug 2022 13:09:00: 7000000 INFO @ Tue, 02 Aug 2022 13:09:03: 16000000 INFO @ Tue, 02 Aug 2022 13:09:05: 12000000 INFO @ Tue, 02 Aug 2022 13:09:07: 8000000 INFO @ Tue, 02 Aug 2022 13:09:09: 17000000 INFO @ Tue, 02 Aug 2022 13:09:12: 13000000 INFO @ Tue, 02 Aug 2022 13:09:14: 9000000 INFO @ Tue, 02 Aug 2022 13:09:16: 18000000 INFO @ Tue, 02 Aug 2022 13:09:19: 14000000 INFO @ Tue, 02 Aug 2022 13:09:21: 10000000 INFO @ Tue, 02 Aug 2022 13:09:23: 19000000 INFO @ Tue, 02 Aug 2022 13:09:26: 15000000 INFO @ Tue, 02 Aug 2022 13:09:27: 11000000 INFO @ Tue, 02 Aug 2022 13:09:30: 20000000 INFO @ Tue, 02 Aug 2022 13:09:33: 16000000 INFO @ Tue, 02 Aug 2022 13:09:34: 12000000 INFO @ Tue, 02 Aug 2022 13:09:37: 21000000 INFO @ Tue, 02 Aug 2022 13:09:40: 17000000 INFO @ Tue, 02 Aug 2022 13:09:41: 13000000 INFO @ Tue, 02 Aug 2022 13:09:44: 22000000 INFO @ Tue, 02 Aug 2022 13:09:47: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:09:48: 14000000 INFO @ Tue, 02 Aug 2022 13:09:51: 23000000 INFO @ Tue, 02 Aug 2022 13:09:54: 19000000 INFO @ Tue, 02 Aug 2022 13:09:55: 15000000 INFO @ Tue, 02 Aug 2022 13:09:58: 24000000 INFO @ Tue, 02 Aug 2022 13:10:00: 20000000 INFO @ Tue, 02 Aug 2022 13:10:02: 16000000 INFO @ Tue, 02 Aug 2022 13:10:05: 25000000 INFO @ Tue, 02 Aug 2022 13:10:07: 21000000 INFO @ Tue, 02 Aug 2022 13:10:09: 17000000 INFO @ Tue, 02 Aug 2022 13:10:12: 26000000 INFO @ Tue, 02 Aug 2022 13:10:14: 22000000 INFO @ Tue, 02 Aug 2022 13:10:16: 18000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:10:18: 27000000 INFO @ Tue, 02 Aug 2022 13:10:21: 23000000 INFO @ Tue, 02 Aug 2022 13:10:23: 19000000 INFO @ Tue, 02 Aug 2022 13:10:25: 28000000 INFO @ Tue, 02 Aug 2022 13:10:28: 24000000 INFO @ Tue, 02 Aug 2022 13:10:30: 20000000 INFO @ Tue, 02 Aug 2022 13:10:32: 29000000 INFO @ Tue, 02 Aug 2022 13:10:35: 25000000 INFO @ Tue, 02 Aug 2022 13:10:36: 21000000 INFO @ Tue, 02 Aug 2022 13:10:39: 30000000 INFO @ Tue, 02 Aug 2022 13:10:39: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 13:10:39: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 13:10:39: #1 total tags in treatment: 14577960 INFO @ Tue, 02 Aug 2022 13:10:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:10:39: #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 13:10:39: #1 tags after filtering in treatment: 10803614 INFO @ Tue, 02 Aug 2022 13:10:39: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 02 Aug 2022 13:10:39: #1 finished! INFO @ Tue, 02 Aug 2022 13:10:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:10:41: #2 number of paired peaks: 12099 INFO @ Tue, 02 Aug 2022 13:10:41: start model_add_line... INFO @ Tue, 02 Aug 2022 13:10:41: start X-correlation... INFO @ Tue, 02 Aug 2022 13:10:41: end of X-cor INFO @ Tue, 02 Aug 2022 13:10:41: #2 finished! INFO @ Tue, 02 Aug 2022 13:10:41: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 13:10:41: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 02 Aug 2022 13:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.05_model.r INFO @ Tue, 02 Aug 2022 13:10:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:10:42: 26000000 INFO @ Tue, 02 Aug 2022 13:10:43: 22000000 INFO @ Tue, 02 Aug 2022 13:10:49: 27000000 INFO @ Tue, 02 Aug 2022 13:10:50: 23000000 INFO @ Tue, 02 Aug 2022 13:10:56: 28000000 INFO @ Tue, 02 Aug 2022 13:10:57: 24000000 INFO @ Tue, 02 Aug 2022 13:11:03: 29000000 INFO @ Tue, 02 Aug 2022 13:11:04: 25000000 INFO @ Tue, 02 Aug 2022 13:11:09: 30000000 INFO @ Tue, 02 Aug 2022 13:11:10: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 13:11:10: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 13:11:10: #1 total tags in treatment: 14577960 INFO @ Tue, 02 Aug 2022 13:11:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:11:10: #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 13:11:10: #1 tags after filtering in treatment: 10803614 INFO @ Tue, 02 Aug 2022 13:11:10: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 02 Aug 2022 13:11:10: #1 finished! INFO @ Tue, 02 Aug 2022 13:11:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:11:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:11:11: 26000000 INFO @ Tue, 02 Aug 2022 13:11:12: #2 number of paired peaks: 12099 INFO @ Tue, 02 Aug 2022 13:11:12: start model_add_line... INFO @ Tue, 02 Aug 2022 13:11:12: start X-correlation... INFO @ Tue, 02 Aug 2022 13:11:12: end of X-cor INFO @ Tue, 02 Aug 2022 13:11:12: #2 finished! INFO @ Tue, 02 Aug 2022 13:11:12: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 13:11:12: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 02 Aug 2022 13:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.10_model.r INFO @ Tue, 02 Aug 2022 13:11:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:11:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:11:18: 27000000 INFO @ Tue, 02 Aug 2022 13:11:24: 28000000 INFO @ Tue, 02 Aug 2022 13:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:11:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.05_summits.bed INFO @ Tue, 02 Aug 2022 13:11:27: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (10096 records, 4 fields): 92 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:11:30: 29000000 INFO @ Tue, 02 Aug 2022 13:11:36: 30000000 INFO @ Tue, 02 Aug 2022 13:11:36: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 13:11:36: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 13:11:36: #1 total tags in treatment: 14577960 INFO @ Tue, 02 Aug 2022 13:11:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:11:36: #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 13:11:36: #1 tags after filtering in treatment: 10803614 INFO @ Tue, 02 Aug 2022 13:11:36: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 02 Aug 2022 13:11:36: #1 finished! INFO @ Tue, 02 Aug 2022 13:11:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:11:38: #2 number of paired peaks: 12099 INFO @ Tue, 02 Aug 2022 13:11:38: start model_add_line... INFO @ Tue, 02 Aug 2022 13:11:38: start X-correlation... INFO @ Tue, 02 Aug 2022 13:11:38: end of X-cor INFO @ Tue, 02 Aug 2022 13:11:38: #2 finished! INFO @ Tue, 02 Aug 2022 13:11:38: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 13:11:38: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 02 Aug 2022 13:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.20_model.r INFO @ Tue, 02 Aug 2022 13:11:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:11:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:11:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.10_summits.bed INFO @ Tue, 02 Aug 2022 13:11:56: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9123 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:12:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:12:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:12:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:12:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847876/ERX5847876.20_summits.bed INFO @ Tue, 02 Aug 2022 13:12:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7506 records, 4 fields): 70 millis CompletedMACS2peakCalling