Job ID = 16440007 SRX = SRX13386236 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 49080393 spots for SRR17206319/SRR17206319.sra Written 49080393 spots for SRR17206319/SRR17206319.sra fastq に変換しました。 bowtie でマッピング中... Your job 16441084 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:46:58 49080393 reads; of these: 49080393 (100.00%) were paired; of these: 3247391 (6.62%) aligned concordantly 0 times 38238384 (77.91%) aligned concordantly exactly 1 time 7594618 (15.47%) aligned concordantly >1 times ---- 3247391 pairs aligned concordantly 0 times; of these: 48776 (1.50%) aligned discordantly 1 time ---- 3198615 pairs aligned 0 times concordantly or discordantly; of these: 6397230 mates make up the pairs; of these: 5228704 (81.73%) aligned 0 times 946294 (14.79%) aligned exactly 1 time 222232 (3.47%) aligned >1 times 94.67% overall alignment rate Time searching: 01:47:00 Overall time: 01:47:00 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 40 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] 25842975 / 45862963 = 0.5635 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 18:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.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 18:53:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:53:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:53:39: 1000000 INFO @ Tue, 02 Aug 2022 18:53:50: 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 18:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.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 18:53:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:53:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:54:02: 3000000 INFO @ Tue, 02 Aug 2022 18:54:07: 1000000 INFO @ Tue, 02 Aug 2022 18:54:14: 4000000 INFO @ Tue, 02 Aug 2022 18:54:18: 2000000 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 18:54:25: 5000000 INFO @ Tue, 02 Aug 2022 18:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.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 18:54:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:54:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:54:30: 3000000 INFO @ Tue, 02 Aug 2022 18:54:37: 6000000 INFO @ Tue, 02 Aug 2022 18:54:38: 1000000 INFO @ Tue, 02 Aug 2022 18:54:41: 4000000 INFO @ Tue, 02 Aug 2022 18:54:50: 7000000 INFO @ Tue, 02 Aug 2022 18:54:52: 2000000 INFO @ Tue, 02 Aug 2022 18:54:52: 5000000 INFO @ Tue, 02 Aug 2022 18:55:02: 8000000 INFO @ Tue, 02 Aug 2022 18:55:04: 6000000 INFO @ Tue, 02 Aug 2022 18:55:05: 3000000 INFO @ Tue, 02 Aug 2022 18:55:15: 7000000 INFO @ Tue, 02 Aug 2022 18:55:15: 9000000 INFO @ Tue, 02 Aug 2022 18:55:18: 4000000 INFO @ Tue, 02 Aug 2022 18:55:26: 8000000 INFO @ Tue, 02 Aug 2022 18:55:27: 10000000 INFO @ Tue, 02 Aug 2022 18:55:31: 5000000 INFO @ Tue, 02 Aug 2022 18:55:37: 9000000 INFO @ Tue, 02 Aug 2022 18:55:40: 11000000 INFO @ Tue, 02 Aug 2022 18:55:44: 6000000 INFO @ Tue, 02 Aug 2022 18:55:48: 10000000 INFO @ Tue, 02 Aug 2022 18:55:52: 12000000 INFO @ Tue, 02 Aug 2022 18:55:56: 7000000 INFO @ Tue, 02 Aug 2022 18:55:59: 11000000 INFO @ Tue, 02 Aug 2022 18:56:05: 13000000 INFO @ Tue, 02 Aug 2022 18:56:09: 8000000 INFO @ Tue, 02 Aug 2022 18:56:10: 12000000 INFO @ Tue, 02 Aug 2022 18:56:18: 14000000 INFO @ Tue, 02 Aug 2022 18:56:21: 13000000 INFO @ Tue, 02 Aug 2022 18:56:22: 9000000 INFO @ Tue, 02 Aug 2022 18:56:31: 15000000 INFO @ Tue, 02 Aug 2022 18:56:32: 14000000 INFO @ Tue, 02 Aug 2022 18:56:34: 10000000 INFO @ Tue, 02 Aug 2022 18:56:44: 15000000 INFO @ Tue, 02 Aug 2022 18:56:44: 16000000 INFO @ Tue, 02 Aug 2022 18:56:47: 11000000 INFO @ Tue, 02 Aug 2022 18:56:55: 16000000 INFO @ Tue, 02 Aug 2022 18:56:56: 17000000 INFO @ Tue, 02 Aug 2022 18:57:00: 12000000 INFO @ Tue, 02 Aug 2022 18:57:06: 17000000 INFO @ Tue, 02 Aug 2022 18:57:10: 18000000 INFO @ Tue, 02 Aug 2022 18:57:13: 13000000 INFO @ Tue, 02 Aug 2022 18:57:17: 18000000 INFO @ Tue, 02 Aug 2022 18:57:23: 19000000 INFO @ Tue, 02 Aug 2022 18:57:26: 14000000 INFO @ Tue, 02 Aug 2022 18:57:29: 19000000 INFO @ Tue, 02 Aug 2022 18:57:36: 20000000 INFO @ Tue, 02 Aug 2022 18:57:39: 15000000 INFO @ Tue, 02 Aug 2022 18:57:40: 20000000 INFO @ Tue, 02 Aug 2022 18:57:49: 21000000 INFO @ Tue, 02 Aug 2022 18:57:52: 21000000 INFO @ Tue, 02 Aug 2022 18:57:52: 16000000 INFO @ Tue, 02 Aug 2022 18:58:02: 22000000 INFO @ Tue, 02 Aug 2022 18:58:03: 22000000 INFO @ Tue, 02 Aug 2022 18:58:04: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:58:14: 23000000 INFO @ Tue, 02 Aug 2022 18:58:14: 23000000 INFO @ Tue, 02 Aug 2022 18:58:17: 18000000 INFO @ Tue, 02 Aug 2022 18:58:25: 24000000 INFO @ Tue, 02 Aug 2022 18:58:26: 24000000 INFO @ Tue, 02 Aug 2022 18:58:30: 19000000 INFO @ Tue, 02 Aug 2022 18:58:36: 25000000 INFO @ Tue, 02 Aug 2022 18:58:39: 25000000 INFO @ Tue, 02 Aug 2022 18:58:44: 20000000 INFO @ Tue, 02 Aug 2022 18:58:47: 26000000 INFO @ Tue, 02 Aug 2022 18:58:52: 26000000 INFO @ Tue, 02 Aug 2022 18:58:57: 21000000 INFO @ Tue, 02 Aug 2022 18:58:58: 27000000 INFO @ Tue, 02 Aug 2022 18:59:04: 27000000 INFO @ Tue, 02 Aug 2022 18:59:08: 28000000 INFO @ Tue, 02 Aug 2022 18:59:10: 22000000 INFO @ Tue, 02 Aug 2022 18:59:16: 28000000 INFO @ Tue, 02 Aug 2022 18:59:19: 29000000 INFO @ Tue, 02 Aug 2022 18:59:22: 23000000 INFO @ Tue, 02 Aug 2022 18:59:28: 29000000 INFO @ Tue, 02 Aug 2022 18:59:30: 30000000 INFO @ Tue, 02 Aug 2022 18:59:35: 24000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:59:40: 30000000 INFO @ Tue, 02 Aug 2022 18:59:42: 31000000 INFO @ Tue, 02 Aug 2022 18:59:47: 25000000 INFO @ Tue, 02 Aug 2022 18:59:53: 32000000 INFO @ Tue, 02 Aug 2022 18:59:53: 31000000 INFO @ Tue, 02 Aug 2022 19:00:00: 26000000 INFO @ Tue, 02 Aug 2022 19:00:04: 33000000 INFO @ Tue, 02 Aug 2022 19:00:07: 32000000 INFO @ Tue, 02 Aug 2022 19:00:12: 27000000 INFO @ Tue, 02 Aug 2022 19:00:15: 34000000 INFO @ Tue, 02 Aug 2022 19:00:19: 33000000 INFO @ Tue, 02 Aug 2022 19:00:25: 28000000 INFO @ Tue, 02 Aug 2022 19:00:25: 35000000 INFO @ Tue, 02 Aug 2022 19:00:32: 34000000 INFO @ Tue, 02 Aug 2022 19:00:36: 36000000 INFO @ Tue, 02 Aug 2022 19:00:38: 29000000 INFO @ Tue, 02 Aug 2022 19:00:44: 35000000 INFO @ Tue, 02 Aug 2022 19:00:47: 37000000 INFO @ Tue, 02 Aug 2022 19:00:50: 30000000 INFO @ Tue, 02 Aug 2022 19:00:57: 36000000 INFO @ Tue, 02 Aug 2022 19:00:59: 38000000 INFO @ Tue, 02 Aug 2022 19:01:04: 31000000 INFO @ Tue, 02 Aug 2022 19:01:09: 37000000 INFO @ Tue, 02 Aug 2022 19:01:10: 39000000 INFO @ Tue, 02 Aug 2022 19:01:17: 32000000 INFO @ Tue, 02 Aug 2022 19:01:20: 40000000 INFO @ Tue, 02 Aug 2022 19:01:22: 38000000 INFO @ Tue, 02 Aug 2022 19:01:30: 33000000 INFO @ Tue, 02 Aug 2022 19:01:31: 41000000 INFO @ Tue, 02 Aug 2022 19:01:34: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 19:01:34: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 19:01:34: #1 total tags in treatment: 20007437 INFO @ Tue, 02 Aug 2022 19:01:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:01:34: #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 19:01:34: #1 tags after filtering in treatment: 13493818 INFO @ Tue, 02 Aug 2022 19:01:34: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 02 Aug 2022 19:01:34: #1 finished! INFO @ Tue, 02 Aug 2022 19:01:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:01:35: 39000000 INFO @ Tue, 02 Aug 2022 19:01:36: #2 number of paired peaks: 1756 INFO @ Tue, 02 Aug 2022 19:01:36: start model_add_line... INFO @ Tue, 02 Aug 2022 19:01:36: start X-correlation... INFO @ Tue, 02 Aug 2022 19:01:36: end of X-cor INFO @ Tue, 02 Aug 2022 19:01:36: #2 finished! INFO @ Tue, 02 Aug 2022 19:01:36: #2 predicted fragment length is 133 bps INFO @ Tue, 02 Aug 2022 19:01:36: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 02 Aug 2022 19:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.10_model.r INFO @ Tue, 02 Aug 2022 19:01:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:01:43: 34000000 INFO @ Tue, 02 Aug 2022 19:01:47: 40000000 INFO @ Tue, 02 Aug 2022 19:01:55: 35000000 INFO @ Tue, 02 Aug 2022 19:02:00: 41000000 INFO @ Tue, 02 Aug 2022 19:02:03: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 19:02:03: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 19:02:03: #1 total tags in treatment: 20007437 INFO @ Tue, 02 Aug 2022 19:02:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:02:03: #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 19:02:03: #1 tags after filtering in treatment: 13493818 INFO @ Tue, 02 Aug 2022 19:02:03: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 02 Aug 2022 19:02:03: #1 finished! INFO @ Tue, 02 Aug 2022 19:02:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:02:04: #2 number of paired peaks: 1756 INFO @ Tue, 02 Aug 2022 19:02:04: start model_add_line... INFO @ Tue, 02 Aug 2022 19:02:05: start X-correlation... INFO @ Tue, 02 Aug 2022 19:02:05: end of X-cor INFO @ Tue, 02 Aug 2022 19:02:05: #2 finished! INFO @ Tue, 02 Aug 2022 19:02:05: #2 predicted fragment length is 133 bps INFO @ Tue, 02 Aug 2022 19:02:05: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 02 Aug 2022 19:02:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.05_model.r INFO @ Tue, 02 Aug 2022 19:02:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:02:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:02:07: 36000000 INFO @ Tue, 02 Aug 2022 19:02:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:02:18: 37000000 INFO @ Tue, 02 Aug 2022 19:02:30: 38000000 INFO @ Tue, 02 Aug 2022 19:02:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.10_peaks.xls INFO @ Tue, 02 Aug 2022 19:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.10_summits.bed INFO @ Tue, 02 Aug 2022 19:02:37: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9063 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 19:02:42: 39000000 INFO @ Tue, 02 Aug 2022 19:02:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:02:53: 40000000 INFO @ Tue, 02 Aug 2022 19:03:05: 41000000 INFO @ Tue, 02 Aug 2022 19:03:07: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 19:03:07: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 19:03:07: #1 total tags in treatment: 20007437 INFO @ Tue, 02 Aug 2022 19:03:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:03:07: #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 19:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.05_peaks.xls INFO @ Tue, 02 Aug 2022 19:03:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:03:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.05_summits.bed INFO @ Tue, 02 Aug 2022 19:03:08: Done! INFO @ Tue, 02 Aug 2022 19:03:08: #1 tags after filtering in treatment: 13493818 INFO @ Tue, 02 Aug 2022 19:03:08: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 02 Aug 2022 19:03:08: #1 finished! INFO @ Tue, 02 Aug 2022 19:03:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:03:08: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (13161 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 19:03:09: #2 number of paired peaks: 1756 INFO @ Tue, 02 Aug 2022 19:03:09: start model_add_line... INFO @ Tue, 02 Aug 2022 19:03:09: start X-correlation... INFO @ Tue, 02 Aug 2022 19:03:09: end of X-cor INFO @ Tue, 02 Aug 2022 19:03:09: #2 finished! INFO @ Tue, 02 Aug 2022 19:03:09: #2 predicted fragment length is 133 bps INFO @ Tue, 02 Aug 2022 19:03:09: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 02 Aug 2022 19:03:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.20_model.r INFO @ Tue, 02 Aug 2022 19:03:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:03:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:04:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.20_peaks.xls INFO @ Tue, 02 Aug 2022 19:04:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:04:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13386236/SRX13386236.20_summits.bed INFO @ Tue, 02 Aug 2022 19:04:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4020 records, 4 fields): 8 millis CompletedMACS2peakCalling