Job ID = 16439383 SRX = SRX15312088 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:01:25 prefetch.2.10.7: 1) Downloading 'SRR19251495'... 2022-08-02T06:01:25 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:02:20 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:02:20 prefetch.2.10.7: 1) 'SRR19251495' was downloaded successfully 2022-08-02T06:02:20 prefetch.2.10.7: 'SRR19251495' has 0 unresolved dependencies Read 24392965 spots for SRR19251495/SRR19251495.sra Written 24392965 spots for SRR19251495/SRR19251495.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439588 ("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: 00:27:01 24392965 reads; of these: 24392965 (100.00%) were paired; of these: 1276513 (5.23%) aligned concordantly 0 times 20940066 (85.84%) aligned concordantly exactly 1 time 2176386 (8.92%) aligned concordantly >1 times ---- 1276513 pairs aligned concordantly 0 times; of these: 247885 (19.42%) aligned discordantly 1 time ---- 1028628 pairs aligned 0 times concordantly or discordantly; of these: 2057256 mates make up the pairs; of these: 1249324 (60.73%) aligned 0 times 591596 (28.76%) aligned exactly 1 time 216336 (10.52%) aligned >1 times 97.44% overall alignment rate Time searching: 00:27:01 Overall time: 00:27:01 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] 2885135 / 23267856 = 0.1240 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 15:47:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.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 15:47:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:47:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:47:44: 1000000 INFO @ Tue, 02 Aug 2022 15:47:52: 2000000 INFO @ Tue, 02 Aug 2022 15:48:00: 3000000 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 15:48:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.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 15:48:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:48:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:48:08: 4000000 INFO @ Tue, 02 Aug 2022 15:48:12: 1000000 INFO @ Tue, 02 Aug 2022 15:48:16: 5000000 INFO @ Tue, 02 Aug 2022 15:48:21: 2000000 INFO @ Tue, 02 Aug 2022 15:48:24: 6000000 INFO @ Tue, 02 Aug 2022 15:48:29: 3000000 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 15:48:33: 7000000 INFO @ Tue, 02 Aug 2022 15:48:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.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 15:48:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:48:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:48:37: 4000000 INFO @ Tue, 02 Aug 2022 15:48:41: 8000000 INFO @ Tue, 02 Aug 2022 15:48:43: 1000000 INFO @ Tue, 02 Aug 2022 15:48:46: 5000000 INFO @ Tue, 02 Aug 2022 15:48:51: 9000000 INFO @ Tue, 02 Aug 2022 15:48:52: 2000000 INFO @ Tue, 02 Aug 2022 15:48:55: 6000000 INFO @ Tue, 02 Aug 2022 15:49:00: 10000000 INFO @ Tue, 02 Aug 2022 15:49:01: 3000000 INFO @ Tue, 02 Aug 2022 15:49:05: 7000000 INFO @ Tue, 02 Aug 2022 15:49:08: 11000000 INFO @ Tue, 02 Aug 2022 15:49:10: 4000000 INFO @ Tue, 02 Aug 2022 15:49:14: 8000000 INFO @ Tue, 02 Aug 2022 15:49:17: 12000000 INFO @ Tue, 02 Aug 2022 15:49:19: 5000000 INFO @ Tue, 02 Aug 2022 15:49:23: 9000000 INFO @ Tue, 02 Aug 2022 15:49:25: 13000000 INFO @ Tue, 02 Aug 2022 15:49:28: 6000000 INFO @ Tue, 02 Aug 2022 15:49:32: 10000000 INFO @ Tue, 02 Aug 2022 15:49:34: 14000000 INFO @ Tue, 02 Aug 2022 15:49:38: 7000000 INFO @ Tue, 02 Aug 2022 15:49:41: 11000000 INFO @ Tue, 02 Aug 2022 15:49:43: 15000000 INFO @ Tue, 02 Aug 2022 15:49:47: 8000000 INFO @ Tue, 02 Aug 2022 15:49:50: 12000000 INFO @ Tue, 02 Aug 2022 15:49:52: 16000000 INFO @ Tue, 02 Aug 2022 15:49:56: 9000000 INFO @ Tue, 02 Aug 2022 15:49:59: 13000000 INFO @ Tue, 02 Aug 2022 15:50:02: 17000000 INFO @ Tue, 02 Aug 2022 15:50:05: 10000000 INFO @ Tue, 02 Aug 2022 15:50:08: 14000000 INFO @ Tue, 02 Aug 2022 15:50:11: 18000000 INFO @ Tue, 02 Aug 2022 15:50:15: 11000000 INFO @ Tue, 02 Aug 2022 15:50:17: 15000000 INFO @ Tue, 02 Aug 2022 15:50:20: 19000000 INFO @ Tue, 02 Aug 2022 15:50:25: 12000000 INFO @ Tue, 02 Aug 2022 15:50:26: 16000000 INFO @ Tue, 02 Aug 2022 15:50:29: 20000000 INFO @ Tue, 02 Aug 2022 15:50:34: 13000000 INFO @ Tue, 02 Aug 2022 15:50:36: 17000000 INFO @ Tue, 02 Aug 2022 15:50:38: 21000000 INFO @ Tue, 02 Aug 2022 15:50:43: 14000000 INFO @ Tue, 02 Aug 2022 15:50:45: 18000000 INFO @ Tue, 02 Aug 2022 15:50:48: 22000000 INFO @ Tue, 02 Aug 2022 15:50:52: 15000000 INFO @ Tue, 02 Aug 2022 15:50:54: 19000000 INFO @ Tue, 02 Aug 2022 15:50:57: 23000000 INFO @ Tue, 02 Aug 2022 15:51:01: 16000000 INFO @ Tue, 02 Aug 2022 15:51:03: 20000000 INFO @ Tue, 02 Aug 2022 15:51:06: 24000000 INFO @ Tue, 02 Aug 2022 15:51:10: 17000000 INFO @ Tue, 02 Aug 2022 15:51:12: 21000000 INFO @ Tue, 02 Aug 2022 15:51:15: 25000000 INFO @ Tue, 02 Aug 2022 15:51:19: 18000000 INFO @ Tue, 02 Aug 2022 15:51:21: 22000000 INFO @ Tue, 02 Aug 2022 15:51:24: 26000000 INFO @ Tue, 02 Aug 2022 15:51:28: 19000000 INFO @ Tue, 02 Aug 2022 15:51:31: 23000000 INFO @ Tue, 02 Aug 2022 15:51:33: 27000000 INFO @ Tue, 02 Aug 2022 15:51:37: 20000000 INFO @ Tue, 02 Aug 2022 15:51:40: 24000000 INFO @ Tue, 02 Aug 2022 15:51:43: 28000000 INFO @ Tue, 02 Aug 2022 15:51:46: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:51:49: 25000000 INFO @ Tue, 02 Aug 2022 15:51:52: 29000000 INFO @ Tue, 02 Aug 2022 15:51:55: 22000000 INFO @ Tue, 02 Aug 2022 15:51:58: 26000000 INFO @ Tue, 02 Aug 2022 15:52:01: 30000000 INFO @ Tue, 02 Aug 2022 15:52:04: 23000000 INFO @ Tue, 02 Aug 2022 15:52:07: 27000000 INFO @ Tue, 02 Aug 2022 15:52:10: 31000000 INFO @ Tue, 02 Aug 2022 15:52:12: 24000000 INFO @ Tue, 02 Aug 2022 15:52:17: 28000000 INFO @ Tue, 02 Aug 2022 15:52:20: 32000000 INFO @ Tue, 02 Aug 2022 15:52:21: 25000000 INFO @ Tue, 02 Aug 2022 15:52:26: 29000000 INFO @ Tue, 02 Aug 2022 15:52:30: 33000000 INFO @ Tue, 02 Aug 2022 15:52:30: 26000000 INFO @ Tue, 02 Aug 2022 15:52:36: 30000000 INFO @ Tue, 02 Aug 2022 15:52:39: 27000000 INFO @ Tue, 02 Aug 2022 15:52:39: 34000000 INFO @ Tue, 02 Aug 2022 15:52:45: 31000000 INFO @ Tue, 02 Aug 2022 15:52:47: 28000000 INFO @ Tue, 02 Aug 2022 15:52:49: 35000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:52:55: 32000000 INFO @ Tue, 02 Aug 2022 15:52:56: 29000000 INFO @ Tue, 02 Aug 2022 15:52:59: 36000000 INFO @ Tue, 02 Aug 2022 15:53:04: 30000000 INFO @ Tue, 02 Aug 2022 15:53:05: 33000000 INFO @ Tue, 02 Aug 2022 15:53:09: 37000000 INFO @ Tue, 02 Aug 2022 15:53:14: 31000000 INFO @ Tue, 02 Aug 2022 15:53:14: 34000000 INFO @ Tue, 02 Aug 2022 15:53:19: 38000000 INFO @ Tue, 02 Aug 2022 15:53:23: 32000000 INFO @ Tue, 02 Aug 2022 15:53:24: 35000000 INFO @ Tue, 02 Aug 2022 15:53:28: 39000000 INFO @ Tue, 02 Aug 2022 15:53:32: 33000000 INFO @ Tue, 02 Aug 2022 15:53:34: 36000000 INFO @ Tue, 02 Aug 2022 15:53:38: 40000000 INFO @ Tue, 02 Aug 2022 15:53:41: 34000000 INFO @ Tue, 02 Aug 2022 15:53:43: 37000000 INFO @ Tue, 02 Aug 2022 15:53:48: 41000000 INFO @ Tue, 02 Aug 2022 15:53:50: 35000000 INFO @ Tue, 02 Aug 2022 15:53:53: 38000000 INFO @ Tue, 02 Aug 2022 15:53:55: #1 tag size is determined as 40 bps INFO @ Tue, 02 Aug 2022 15:53:55: #1 tag size = 40 INFO @ Tue, 02 Aug 2022 15:53:55: #1 total tags in treatment: 20236168 INFO @ Tue, 02 Aug 2022 15:53:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:53:55: #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 15:53:56: #1 tags after filtering in treatment: 11535111 INFO @ Tue, 02 Aug 2022 15:53:56: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 02 Aug 2022 15:53:56: #1 finished! INFO @ Tue, 02 Aug 2022 15:53:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:53:57: #2 number of paired peaks: 4718 INFO @ Tue, 02 Aug 2022 15:53:57: start model_add_line... INFO @ Tue, 02 Aug 2022 15:53:57: start X-correlation... INFO @ Tue, 02 Aug 2022 15:53:58: end of X-cor INFO @ Tue, 02 Aug 2022 15:53:58: #2 finished! INFO @ Tue, 02 Aug 2022 15:53:58: #2 predicted fragment length is 102 bps INFO @ Tue, 02 Aug 2022 15:53:58: #2 alternative fragment length(s) may be 102 bps INFO @ Tue, 02 Aug 2022 15:53:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.05_model.r INFO @ Tue, 02 Aug 2022 15:53:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:53:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:53:59: 36000000 INFO @ Tue, 02 Aug 2022 15:54:02: 39000000 INFO @ Tue, 02 Aug 2022 15:54:07: 37000000 INFO @ Tue, 02 Aug 2022 15:54:10: 40000000 INFO @ Tue, 02 Aug 2022 15:54:16: 38000000 INFO @ Tue, 02 Aug 2022 15:54:19: 41000000 INFO @ Tue, 02 Aug 2022 15:54:25: 39000000 INFO @ Tue, 02 Aug 2022 15:54:26: #1 tag size is determined as 40 bps INFO @ Tue, 02 Aug 2022 15:54:26: #1 tag size = 40 INFO @ Tue, 02 Aug 2022 15:54:26: #1 total tags in treatment: 20236168 INFO @ Tue, 02 Aug 2022 15:54:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:54:26: #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 15:54:27: #1 tags after filtering in treatment: 11535111 INFO @ Tue, 02 Aug 2022 15:54:27: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 02 Aug 2022 15:54:27: #1 finished! INFO @ Tue, 02 Aug 2022 15:54:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:54:29: #2 number of paired peaks: 4718 INFO @ Tue, 02 Aug 2022 15:54:29: start model_add_line... INFO @ Tue, 02 Aug 2022 15:54:29: start X-correlation... INFO @ Tue, 02 Aug 2022 15:54:29: end of X-cor INFO @ Tue, 02 Aug 2022 15:54:29: #2 finished! INFO @ Tue, 02 Aug 2022 15:54:29: #2 predicted fragment length is 102 bps INFO @ Tue, 02 Aug 2022 15:54:29: #2 alternative fragment length(s) may be 102 bps INFO @ Tue, 02 Aug 2022 15:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.10_model.r INFO @ Tue, 02 Aug 2022 15:54:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:54:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:54:33: 40000000 INFO @ Tue, 02 Aug 2022 15:54:41: 41000000 INFO @ Tue, 02 Aug 2022 15:54:47: #1 tag size is determined as 40 bps INFO @ Tue, 02 Aug 2022 15:54:47: #1 tag size = 40 INFO @ Tue, 02 Aug 2022 15:54:47: #1 total tags in treatment: 20236168 INFO @ Tue, 02 Aug 2022 15:54:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:54:47: #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 15:54:47: #1 tags after filtering in treatment: 11535111 INFO @ Tue, 02 Aug 2022 15:54:47: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 02 Aug 2022 15:54:47: #1 finished! INFO @ Tue, 02 Aug 2022 15:54:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:54:49: #2 number of paired peaks: 4718 INFO @ Tue, 02 Aug 2022 15:54:49: start model_add_line... INFO @ Tue, 02 Aug 2022 15:54:49: start X-correlation... INFO @ Tue, 02 Aug 2022 15:54:49: end of X-cor INFO @ Tue, 02 Aug 2022 15:54:49: #2 finished! INFO @ Tue, 02 Aug 2022 15:54:49: #2 predicted fragment length is 102 bps INFO @ Tue, 02 Aug 2022 15:54:49: #2 alternative fragment length(s) may be 102 bps INFO @ Tue, 02 Aug 2022 15:54:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.20_model.r INFO @ Tue, 02 Aug 2022 15:54:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:54:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:54:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:54:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:54:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.05_summits.bed INFO @ Tue, 02 Aug 2022 15:54:54: Done! pass1 - making usageList (14 chroms): 8 millis pass2 - checking and writing primary data (18997 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:55:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:55:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:55:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:55:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:55:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.10_summits.bed INFO @ Tue, 02 Aug 2022 15:55:23: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (13565 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:55:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:55:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:55:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15312088/SRX15312088.20_summits.bed INFO @ Tue, 02 Aug 2022 15:55:43: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (6326 records, 4 fields): 27 millis CompletedMACS2peakCalling