Job ID = 16439592 SRX = SRX9518338 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24167348 spots for SRR13070821/SRR13070821.sra Written 24167348 spots for SRR13070821/SRR13070821.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439859 ("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: 00:39:55 24167348 reads; of these: 24167348 (100.00%) were paired; of these: 4418139 (18.28%) aligned concordantly 0 times 17804651 (73.67%) aligned concordantly exactly 1 time 1944558 (8.05%) aligned concordantly >1 times ---- 4418139 pairs aligned concordantly 0 times; of these: 340582 (7.71%) aligned discordantly 1 time ---- 4077557 pairs aligned 0 times concordantly or discordantly; of these: 8155114 mates make up the pairs; of these: 7492749 (91.88%) aligned 0 times 458710 (5.62%) aligned exactly 1 time 203655 (2.50%) aligned >1 times 84.50% overall alignment rate Time searching: 00:39:55 Overall time: 00:39:55 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 20 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] 2974118 / 20031082 = 0.1485 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 16:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.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 16:34:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:34:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:34:39: 1000000 INFO @ Tue, 02 Aug 2022 16:34:47: 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 16:34:56: 3000000 INFO @ Tue, 02 Aug 2022 16:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.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 16:34:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:34:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:35:05: 4000000 INFO @ Tue, 02 Aug 2022 16:35:08: 1000000 INFO @ Tue, 02 Aug 2022 16:35:14: 5000000 INFO @ Tue, 02 Aug 2022 16:35:17: 2000000 INFO @ Tue, 02 Aug 2022 16:35:23: 6000000 INFO @ Tue, 02 Aug 2022 16:35:26: 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 16:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.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 16:35:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:35:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:35:32: 7000000 INFO @ Tue, 02 Aug 2022 16:35:35: 4000000 INFO @ Tue, 02 Aug 2022 16:35:38: 1000000 INFO @ Tue, 02 Aug 2022 16:35:41: 8000000 INFO @ Tue, 02 Aug 2022 16:35:44: 5000000 INFO @ Tue, 02 Aug 2022 16:35:47: 2000000 INFO @ Tue, 02 Aug 2022 16:35:51: 9000000 INFO @ Tue, 02 Aug 2022 16:35:53: 6000000 INFO @ Tue, 02 Aug 2022 16:35:56: 3000000 INFO @ Tue, 02 Aug 2022 16:36:00: 10000000 INFO @ Tue, 02 Aug 2022 16:36:02: 7000000 INFO @ Tue, 02 Aug 2022 16:36:05: 4000000 INFO @ Tue, 02 Aug 2022 16:36:09: 11000000 INFO @ Tue, 02 Aug 2022 16:36:12: 8000000 INFO @ Tue, 02 Aug 2022 16:36:15: 5000000 INFO @ Tue, 02 Aug 2022 16:36:18: 12000000 INFO @ Tue, 02 Aug 2022 16:36:21: 9000000 INFO @ Tue, 02 Aug 2022 16:36:23: 6000000 INFO @ Tue, 02 Aug 2022 16:36:27: 13000000 INFO @ Tue, 02 Aug 2022 16:36:30: 10000000 INFO @ Tue, 02 Aug 2022 16:36:32: 7000000 INFO @ Tue, 02 Aug 2022 16:36:36: 14000000 INFO @ Tue, 02 Aug 2022 16:36:39: 11000000 INFO @ Tue, 02 Aug 2022 16:36:41: 8000000 INFO @ Tue, 02 Aug 2022 16:36:45: 15000000 INFO @ Tue, 02 Aug 2022 16:36:48: 12000000 INFO @ Tue, 02 Aug 2022 16:36:50: 9000000 INFO @ Tue, 02 Aug 2022 16:36:54: 16000000 INFO @ Tue, 02 Aug 2022 16:36:57: 13000000 INFO @ Tue, 02 Aug 2022 16:36:59: 10000000 INFO @ Tue, 02 Aug 2022 16:37:03: 17000000 INFO @ Tue, 02 Aug 2022 16:37:05: 14000000 INFO @ Tue, 02 Aug 2022 16:37:08: 11000000 INFO @ Tue, 02 Aug 2022 16:37:12: 18000000 INFO @ Tue, 02 Aug 2022 16:37:14: 15000000 INFO @ Tue, 02 Aug 2022 16:37:17: 12000000 INFO @ Tue, 02 Aug 2022 16:37:21: 19000000 INFO @ Tue, 02 Aug 2022 16:37:23: 16000000 INFO @ Tue, 02 Aug 2022 16:37:27: 13000000 INFO @ Tue, 02 Aug 2022 16:37:30: 20000000 INFO @ Tue, 02 Aug 2022 16:37:32: 17000000 INFO @ Tue, 02 Aug 2022 16:37:36: 14000000 INFO @ Tue, 02 Aug 2022 16:37:39: 21000000 INFO @ Tue, 02 Aug 2022 16:37:41: 18000000 INFO @ Tue, 02 Aug 2022 16:37:45: 15000000 INFO @ Tue, 02 Aug 2022 16:37:47: 22000000 INFO @ Tue, 02 Aug 2022 16:37:49: 19000000 INFO @ Tue, 02 Aug 2022 16:37:54: 16000000 INFO @ Tue, 02 Aug 2022 16:37:56: 23000000 INFO @ Tue, 02 Aug 2022 16:37:58: 20000000 INFO @ Tue, 02 Aug 2022 16:38:02: 17000000 INFO @ Tue, 02 Aug 2022 16:38:05: 24000000 INFO @ Tue, 02 Aug 2022 16:38:08: 21000000 INFO @ Tue, 02 Aug 2022 16:38:11: 18000000 INFO @ Tue, 02 Aug 2022 16:38:14: 25000000 INFO @ Tue, 02 Aug 2022 16:38:17: 22000000 INFO @ Tue, 02 Aug 2022 16:38:20: 19000000 INFO @ Tue, 02 Aug 2022 16:38:22: 26000000 INFO @ Tue, 02 Aug 2022 16:38:26: 23000000 INFO @ Tue, 02 Aug 2022 16:38:28: 20000000 INFO @ Tue, 02 Aug 2022 16:38:31: 27000000 INFO @ Tue, 02 Aug 2022 16:38:35: 24000000 INFO @ Tue, 02 Aug 2022 16:38:37: 21000000 INFO @ Tue, 02 Aug 2022 16:38:40: 28000000 INFO @ Tue, 02 Aug 2022 16:38:44: 25000000 INFO @ Tue, 02 Aug 2022 16:38:46: 22000000 INFO @ Tue, 02 Aug 2022 16:38:49: 29000000 INFO @ Tue, 02 Aug 2022 16:38:52: 26000000 INFO @ Tue, 02 Aug 2022 16:38:54: 23000000 INFO @ Tue, 02 Aug 2022 16:38:58: 30000000 INFO @ Tue, 02 Aug 2022 16:39:01: 27000000 INFO @ Tue, 02 Aug 2022 16:39:03: 24000000 INFO @ Tue, 02 Aug 2022 16:39:07: 31000000 INFO @ Tue, 02 Aug 2022 16:39:10: 28000000 INFO @ Tue, 02 Aug 2022 16:39:13: 25000000 INFO @ Tue, 02 Aug 2022 16:39:16: 32000000 INFO @ Tue, 02 Aug 2022 16:39:19: 29000000 INFO @ Tue, 02 Aug 2022 16:39:22: 26000000 INFO @ Tue, 02 Aug 2022 16:39:25: 33000000 INFO @ Tue, 02 Aug 2022 16:39:28: 30000000 INFO @ Tue, 02 Aug 2022 16:39:30: 27000000 INFO @ Tue, 02 Aug 2022 16:39:34: 34000000 INFO @ Tue, 02 Aug 2022 16:39:37: 31000000 INFO @ Tue, 02 Aug 2022 16:39:39: 28000000 INFO @ Tue, 02 Aug 2022 16:39:42: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:39:42: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:39:42: #1 total tags in treatment: 16791555 INFO @ Tue, 02 Aug 2022 16:39:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:39:42: #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 16:39:43: #1 tags after filtering in treatment: 9971833 INFO @ Tue, 02 Aug 2022 16:39:43: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 02 Aug 2022 16:39:43: #1 finished! INFO @ Tue, 02 Aug 2022 16:39:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:39:44: #2 number of paired peaks: 9026 INFO @ Tue, 02 Aug 2022 16:39:44: start model_add_line... INFO @ Tue, 02 Aug 2022 16:39:44: start X-correlation... INFO @ Tue, 02 Aug 2022 16:39:45: end of X-cor INFO @ Tue, 02 Aug 2022 16:39:45: #2 finished! INFO @ Tue, 02 Aug 2022 16:39:45: #2 predicted fragment length is 209 bps INFO @ Tue, 02 Aug 2022 16:39:45: #2 alternative fragment length(s) may be 209 bps INFO @ Tue, 02 Aug 2022 16:39:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.05_model.r INFO @ Tue, 02 Aug 2022 16:39:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:39:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:39:46: 32000000 INFO @ Tue, 02 Aug 2022 16:39:48: 29000000 INFO @ Tue, 02 Aug 2022 16:39:55: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:39:57: 30000000 INFO @ Tue, 02 Aug 2022 16:40:04: 34000000 INFO @ Tue, 02 Aug 2022 16:40:06: 31000000 INFO @ Tue, 02 Aug 2022 16:40:12: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:40:12: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:40:12: #1 total tags in treatment: 16791555 INFO @ Tue, 02 Aug 2022 16:40:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:40:12: #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 16:40:12: #1 tags after filtering in treatment: 9971833 INFO @ Tue, 02 Aug 2022 16:40:12: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 02 Aug 2022 16:40:12: #1 finished! INFO @ Tue, 02 Aug 2022 16:40:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:40:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:40:14: 32000000 INFO @ Tue, 02 Aug 2022 16:40:14: #2 number of paired peaks: 9026 INFO @ Tue, 02 Aug 2022 16:40:14: start model_add_line... INFO @ Tue, 02 Aug 2022 16:40:14: start X-correlation... INFO @ Tue, 02 Aug 2022 16:40:14: end of X-cor INFO @ Tue, 02 Aug 2022 16:40:14: #2 finished! INFO @ Tue, 02 Aug 2022 16:40:14: #2 predicted fragment length is 209 bps INFO @ Tue, 02 Aug 2022 16:40:14: #2 alternative fragment length(s) may be 209 bps INFO @ Tue, 02 Aug 2022 16:40:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.10_model.r INFO @ Tue, 02 Aug 2022 16:40:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:40:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:40:22: 33000000 INFO @ Tue, 02 Aug 2022 16:40:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:40:31: 34000000 INFO @ Tue, 02 Aug 2022 16:40:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:40:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:40:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.05_summits.bed INFO @ Tue, 02 Aug 2022 16:40:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6099 records, 4 fields): 32 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:40:38: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:40:38: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:40:38: #1 total tags in treatment: 16791555 INFO @ Tue, 02 Aug 2022 16:40:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:40:38: #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 16:40:38: #1 tags after filtering in treatment: 9971833 INFO @ Tue, 02 Aug 2022 16:40:38: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 02 Aug 2022 16:40:38: #1 finished! INFO @ Tue, 02 Aug 2022 16:40:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:40:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:40:40: #2 number of paired peaks: 9026 INFO @ Tue, 02 Aug 2022 16:40:40: start model_add_line... INFO @ Tue, 02 Aug 2022 16:40:40: start X-correlation... INFO @ Tue, 02 Aug 2022 16:40:40: end of X-cor INFO @ Tue, 02 Aug 2022 16:40:40: #2 finished! INFO @ Tue, 02 Aug 2022 16:40:40: #2 predicted fragment length is 209 bps INFO @ Tue, 02 Aug 2022 16:40:40: #2 alternative fragment length(s) may be 209 bps INFO @ Tue, 02 Aug 2022 16:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.20_model.r INFO @ Tue, 02 Aug 2022 16:40:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:40:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:40:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:41:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:41:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:41:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.10_summits.bed INFO @ Tue, 02 Aug 2022 16:41:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5714 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:41:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:41:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:41:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:41:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518338/SRX9518338.20_summits.bed INFO @ Tue, 02 Aug 2022 16:41:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5211 records, 4 fields): 128 millis CompletedMACS2peakCalling