Job ID = 16439387 SRX = SRX15312089 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:01:37 prefetch.2.10.7: 1) Downloading 'SRR19251494'... 2022-08-02T06:01:37 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:02:24 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:02:24 prefetch.2.10.7: 1) 'SRR19251494' was downloaded successfully 2022-08-02T06:02:24 prefetch.2.10.7: 'SRR19251494' has 0 unresolved dependencies Read 22625222 spots for SRR19251494/SRR19251494.sra Written 22625222 spots for SRR19251494/SRR19251494.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439510 ("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: 00:16:53 22625222 reads; of these: 22625222 (100.00%) were paired; of these: 1050698 (4.64%) aligned concordantly 0 times 18668585 (82.51%) aligned concordantly exactly 1 time 2905939 (12.84%) aligned concordantly >1 times ---- 1050698 pairs aligned concordantly 0 times; of these: 171540 (16.33%) aligned discordantly 1 time ---- 879158 pairs aligned 0 times concordantly or discordantly; of these: 1758316 mates make up the pairs; of these: 1186286 (67.47%) aligned 0 times 433990 (24.68%) aligned exactly 1 time 138040 (7.85%) aligned >1 times 97.38% overall alignment rate Time searching: 00:16:53 Overall time: 00:16:53 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] 3252706 / 21617056 = 0.1505 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 15:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.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 15:30:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:30:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:30:49: 1000000 INFO @ Tue, 02 Aug 2022 15:30:55: 2000000 INFO @ Tue, 02 Aug 2022 15:31:01: 3000000 INFO @ Tue, 02 Aug 2022 15:31:07: 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 15:31:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.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 15:31:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:31:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:31:13: 5000000 INFO @ Tue, 02 Aug 2022 15:31:18: 1000000 INFO @ Tue, 02 Aug 2022 15:31:20: 6000000 INFO @ Tue, 02 Aug 2022 15:31:25: 2000000 INFO @ Tue, 02 Aug 2022 15:31:27: 7000000 INFO @ Tue, 02 Aug 2022 15:31:31: 3000000 INFO @ Tue, 02 Aug 2022 15:31:33: 8000000 INFO @ Tue, 02 Aug 2022 15:31:37: 4000000 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 15:31:40: 9000000 INFO @ Tue, 02 Aug 2022 15:31:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.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 15:31:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:31:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:31:44: 5000000 INFO @ Tue, 02 Aug 2022 15:31:47: 10000000 INFO @ Tue, 02 Aug 2022 15:31:49: 1000000 INFO @ Tue, 02 Aug 2022 15:31:51: 6000000 INFO @ Tue, 02 Aug 2022 15:31:54: 11000000 INFO @ Tue, 02 Aug 2022 15:31:56: 2000000 INFO @ Tue, 02 Aug 2022 15:31:57: 7000000 INFO @ Tue, 02 Aug 2022 15:32:01: 12000000 INFO @ Tue, 02 Aug 2022 15:32:03: 3000000 INFO @ Tue, 02 Aug 2022 15:32:04: 8000000 INFO @ Tue, 02 Aug 2022 15:32:08: 13000000 INFO @ Tue, 02 Aug 2022 15:32:10: 4000000 INFO @ Tue, 02 Aug 2022 15:32:11: 9000000 INFO @ Tue, 02 Aug 2022 15:32:15: 14000000 INFO @ Tue, 02 Aug 2022 15:32:16: 5000000 INFO @ Tue, 02 Aug 2022 15:32:17: 10000000 INFO @ Tue, 02 Aug 2022 15:32:22: 15000000 INFO @ Tue, 02 Aug 2022 15:32:23: 6000000 INFO @ Tue, 02 Aug 2022 15:32:24: 11000000 INFO @ Tue, 02 Aug 2022 15:32:29: 16000000 INFO @ Tue, 02 Aug 2022 15:32:30: 7000000 INFO @ Tue, 02 Aug 2022 15:32:31: 12000000 INFO @ Tue, 02 Aug 2022 15:32:36: 17000000 INFO @ Tue, 02 Aug 2022 15:32:37: 8000000 INFO @ Tue, 02 Aug 2022 15:32:38: 13000000 INFO @ Tue, 02 Aug 2022 15:32:42: 18000000 INFO @ Tue, 02 Aug 2022 15:32:43: 9000000 INFO @ Tue, 02 Aug 2022 15:32:45: 14000000 INFO @ Tue, 02 Aug 2022 15:32:49: 19000000 INFO @ Tue, 02 Aug 2022 15:32:50: 10000000 INFO @ Tue, 02 Aug 2022 15:32:51: 15000000 INFO @ Tue, 02 Aug 2022 15:32:55: 20000000 INFO @ Tue, 02 Aug 2022 15:32:56: 11000000 INFO @ Tue, 02 Aug 2022 15:32:58: 16000000 INFO @ Tue, 02 Aug 2022 15:33:02: 21000000 INFO @ Tue, 02 Aug 2022 15:33:03: 12000000 INFO @ Tue, 02 Aug 2022 15:33:05: 17000000 INFO @ Tue, 02 Aug 2022 15:33:09: 22000000 INFO @ Tue, 02 Aug 2022 15:33:10: 13000000 INFO @ Tue, 02 Aug 2022 15:33:11: 18000000 INFO @ Tue, 02 Aug 2022 15:33:15: 23000000 INFO @ Tue, 02 Aug 2022 15:33:16: 14000000 INFO @ Tue, 02 Aug 2022 15:33:18: 19000000 INFO @ Tue, 02 Aug 2022 15:33:22: 24000000 INFO @ Tue, 02 Aug 2022 15:33:23: 15000000 INFO @ Tue, 02 Aug 2022 15:33:25: 20000000 INFO @ Tue, 02 Aug 2022 15:33:28: 25000000 INFO @ Tue, 02 Aug 2022 15:33:29: 16000000 INFO @ Tue, 02 Aug 2022 15:33:31: 21000000 INFO @ Tue, 02 Aug 2022 15:33:35: 26000000 INFO @ Tue, 02 Aug 2022 15:33:36: 17000000 INFO @ Tue, 02 Aug 2022 15:33:38: 22000000 INFO @ Tue, 02 Aug 2022 15:33:42: 27000000 INFO @ Tue, 02 Aug 2022 15:33:42: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:33:45: 23000000 INFO @ Tue, 02 Aug 2022 15:33:48: 28000000 INFO @ Tue, 02 Aug 2022 15:33:49: 19000000 INFO @ Tue, 02 Aug 2022 15:33:51: 24000000 INFO @ Tue, 02 Aug 2022 15:33:55: 29000000 INFO @ Tue, 02 Aug 2022 15:33:56: 20000000 INFO @ Tue, 02 Aug 2022 15:33:58: 25000000 INFO @ Tue, 02 Aug 2022 15:34:02: 30000000 INFO @ Tue, 02 Aug 2022 15:34:02: 21000000 INFO @ Tue, 02 Aug 2022 15:34:05: 26000000 INFO @ Tue, 02 Aug 2022 15:34:09: 31000000 INFO @ Tue, 02 Aug 2022 15:34:09: 22000000 INFO @ Tue, 02 Aug 2022 15:34:11: 27000000 INFO @ Tue, 02 Aug 2022 15:34:15: 32000000 INFO @ Tue, 02 Aug 2022 15:34:16: 23000000 INFO @ Tue, 02 Aug 2022 15:34:18: 28000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:34:22: 33000000 INFO @ Tue, 02 Aug 2022 15:34:22: 24000000 INFO @ Tue, 02 Aug 2022 15:34:25: 29000000 INFO @ Tue, 02 Aug 2022 15:34:29: 34000000 INFO @ Tue, 02 Aug 2022 15:34:29: 25000000 INFO @ Tue, 02 Aug 2022 15:34:32: 30000000 INFO @ Tue, 02 Aug 2022 15:34:35: 35000000 INFO @ Tue, 02 Aug 2022 15:34:36: 26000000 INFO @ Tue, 02 Aug 2022 15:34:39: 31000000 INFO @ Tue, 02 Aug 2022 15:34:42: 36000000 INFO @ Tue, 02 Aug 2022 15:34:42: 27000000 INFO @ Tue, 02 Aug 2022 15:34:45: 32000000 INFO @ Tue, 02 Aug 2022 15:34:49: 37000000 INFO @ Tue, 02 Aug 2022 15:34:49: 28000000 INFO @ Tue, 02 Aug 2022 15:34:52: 33000000 INFO @ Tue, 02 Aug 2022 15:34:52: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 15:34:52: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 15:34:52: #1 total tags in treatment: 18325290 INFO @ Tue, 02 Aug 2022 15:34:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:34:52: #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 15:34:53: #1 tags after filtering in treatment: 10868560 INFO @ Tue, 02 Aug 2022 15:34:53: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 02 Aug 2022 15:34:53: #1 finished! INFO @ Tue, 02 Aug 2022 15:34:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:34:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:34:54: #2 number of paired peaks: 4266 INFO @ Tue, 02 Aug 2022 15:34:54: start model_add_line... INFO @ Tue, 02 Aug 2022 15:34:54: start X-correlation... INFO @ Tue, 02 Aug 2022 15:34:54: end of X-cor INFO @ Tue, 02 Aug 2022 15:34:54: #2 finished! INFO @ Tue, 02 Aug 2022 15:34:54: #2 predicted fragment length is 94 bps INFO @ Tue, 02 Aug 2022 15:34:54: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 02 Aug 2022 15:34:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.05_model.r INFO @ Tue, 02 Aug 2022 15:34:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:34:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:34:56: 29000000 INFO @ Tue, 02 Aug 2022 15:34:59: 34000000 INFO @ Tue, 02 Aug 2022 15:35:02: 30000000 INFO @ Tue, 02 Aug 2022 15:35:05: 35000000 INFO @ Tue, 02 Aug 2022 15:35:09: 31000000 INFO @ Tue, 02 Aug 2022 15:35:12: 36000000 INFO @ Tue, 02 Aug 2022 15:35:15: 32000000 INFO @ Tue, 02 Aug 2022 15:35:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:35:19: 37000000 INFO @ Tue, 02 Aug 2022 15:35:22: 33000000 INFO @ Tue, 02 Aug 2022 15:35:23: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 15:35:23: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 15:35:23: #1 total tags in treatment: 18325290 INFO @ Tue, 02 Aug 2022 15:35:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:35:23: #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 15:35:23: #1 tags after filtering in treatment: 10868560 INFO @ Tue, 02 Aug 2022 15:35:23: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 02 Aug 2022 15:35:23: #1 finished! INFO @ Tue, 02 Aug 2022 15:35:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:35:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:35:24: #2 number of paired peaks: 4266 INFO @ Tue, 02 Aug 2022 15:35:24: start model_add_line... INFO @ Tue, 02 Aug 2022 15:35:25: start X-correlation... INFO @ Tue, 02 Aug 2022 15:35:25: end of X-cor INFO @ Tue, 02 Aug 2022 15:35:25: #2 finished! INFO @ Tue, 02 Aug 2022 15:35:25: #2 predicted fragment length is 94 bps INFO @ Tue, 02 Aug 2022 15:35:25: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 02 Aug 2022 15:35:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.10_model.r INFO @ Tue, 02 Aug 2022 15:35:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:35:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:35:28: 34000000 INFO @ Tue, 02 Aug 2022 15:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.05_summits.bed INFO @ Tue, 02 Aug 2022 15:35:29: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (20119 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:35:34: 35000000 INFO @ Tue, 02 Aug 2022 15:35:39: 36000000 INFO @ Tue, 02 Aug 2022 15:35:46: 37000000 INFO @ Tue, 02 Aug 2022 15:35:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:35:49: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 15:35:49: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 15:35:49: #1 total tags in treatment: 18325290 INFO @ Tue, 02 Aug 2022 15:35:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:35:49: #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 15:35:50: #1 tags after filtering in treatment: 10868560 INFO @ Tue, 02 Aug 2022 15:35:50: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 02 Aug 2022 15:35:50: #1 finished! INFO @ Tue, 02 Aug 2022 15:35:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:35:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:35:51: #2 number of paired peaks: 4266 INFO @ Tue, 02 Aug 2022 15:35:51: start model_add_line... INFO @ Tue, 02 Aug 2022 15:35:51: start X-correlation... INFO @ Tue, 02 Aug 2022 15:35:51: end of X-cor INFO @ Tue, 02 Aug 2022 15:35:51: #2 finished! INFO @ Tue, 02 Aug 2022 15:35:51: #2 predicted fragment length is 94 bps INFO @ Tue, 02 Aug 2022 15:35:51: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 02 Aug 2022 15:35:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.20_model.r INFO @ Tue, 02 Aug 2022 15:35:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:35:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:35:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:35:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:35:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.10_summits.bed INFO @ Tue, 02 Aug 2022 15:35:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (13336 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:36:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:36:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:36:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:36:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15312089/SRX15312089.20_summits.bed INFO @ Tue, 02 Aug 2022 15:36:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5368 records, 4 fields): 32 millis CompletedMACS2peakCalling