Job ID = 6626557 SRX = SRX7224526 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18053985 spots for SRR10541178/SRR10541178.sra Written 18053985 spots for SRR10541178/SRR10541178.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627132 ("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: 01:45:50 18053985 reads; of these: 18053985 (100.00%) were paired; of these: 1928863 (10.68%) aligned concordantly 0 times 4682886 (25.94%) aligned concordantly exactly 1 time 11442236 (63.38%) aligned concordantly >1 times ---- 1928863 pairs aligned concordantly 0 times; of these: 25939 (1.34%) aligned discordantly 1 time ---- 1902924 pairs aligned 0 times concordantly or discordantly; of these: 3805848 mates make up the pairs; of these: 1897228 (49.85%) aligned 0 times 299858 (7.88%) aligned exactly 1 time 1608762 (42.27%) aligned >1 times 94.75% overall alignment rate Time searching: 01:45:50 Overall time: 01:45:50 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] 936062 / 16102101 = 0.0581 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:28:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.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, 14 Jul 2020 09:28:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:28:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:28:43: 1000000 INFO @ Tue, 14 Jul 2020 09:28:49: 2000000 INFO @ Tue, 14 Jul 2020 09:28:54: 3000000 INFO @ Tue, 14 Jul 2020 09:29:00: 4000000 INFO @ Tue, 14 Jul 2020 09:29:06: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.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, 14 Jul 2020 09:29:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:29:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:29:12: 6000000 INFO @ Tue, 14 Jul 2020 09:29:14: 1000000 INFO @ Tue, 14 Jul 2020 09:29:18: 7000000 INFO @ Tue, 14 Jul 2020 09:29:21: 2000000 INFO @ Tue, 14 Jul 2020 09:29:24: 8000000 INFO @ Tue, 14 Jul 2020 09:29:27: 3000000 INFO @ Tue, 14 Jul 2020 09:29:32: 9000000 INFO @ Tue, 14 Jul 2020 09:29:33: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.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, 14 Jul 2020 09:29:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:29:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:29:39: 10000000 INFO @ Tue, 14 Jul 2020 09:29:40: 5000000 INFO @ Tue, 14 Jul 2020 09:29:45: 1000000 INFO @ Tue, 14 Jul 2020 09:29:45: 11000000 INFO @ Tue, 14 Jul 2020 09:29:46: 6000000 INFO @ Tue, 14 Jul 2020 09:29:52: 12000000 INFO @ Tue, 14 Jul 2020 09:29:52: 2000000 INFO @ Tue, 14 Jul 2020 09:29:53: 7000000 INFO @ Tue, 14 Jul 2020 09:29:58: 13000000 INFO @ Tue, 14 Jul 2020 09:29:59: 8000000 INFO @ Tue, 14 Jul 2020 09:29:59: 3000000 INFO @ Tue, 14 Jul 2020 09:30:04: 14000000 INFO @ Tue, 14 Jul 2020 09:30:06: 9000000 INFO @ Tue, 14 Jul 2020 09:30:07: 4000000 INFO @ Tue, 14 Jul 2020 09:30:11: 15000000 INFO @ Tue, 14 Jul 2020 09:30:12: 10000000 INFO @ Tue, 14 Jul 2020 09:30:14: 5000000 INFO @ Tue, 14 Jul 2020 09:30:17: 16000000 INFO @ Tue, 14 Jul 2020 09:30:19: 11000000 INFO @ Tue, 14 Jul 2020 09:30:21: 6000000 INFO @ Tue, 14 Jul 2020 09:30:24: 17000000 INFO @ Tue, 14 Jul 2020 09:30:25: 12000000 INFO @ Tue, 14 Jul 2020 09:30:29: 7000000 INFO @ Tue, 14 Jul 2020 09:30:30: 18000000 INFO @ Tue, 14 Jul 2020 09:30:31: 13000000 INFO @ Tue, 14 Jul 2020 09:30:36: 8000000 INFO @ Tue, 14 Jul 2020 09:30:37: 19000000 INFO @ Tue, 14 Jul 2020 09:30:38: 14000000 INFO @ Tue, 14 Jul 2020 09:30:43: 9000000 INFO @ Tue, 14 Jul 2020 09:30:43: 20000000 INFO @ Tue, 14 Jul 2020 09:30:44: 15000000 INFO @ Tue, 14 Jul 2020 09:30:50: 21000000 INFO @ Tue, 14 Jul 2020 09:30:50: 10000000 INFO @ Tue, 14 Jul 2020 09:30:51: 16000000 INFO @ Tue, 14 Jul 2020 09:30:56: 22000000 INFO @ Tue, 14 Jul 2020 09:30:57: 17000000 INFO @ Tue, 14 Jul 2020 09:30:58: 11000000 INFO @ Tue, 14 Jul 2020 09:31:03: 23000000 INFO @ Tue, 14 Jul 2020 09:31:04: 18000000 INFO @ Tue, 14 Jul 2020 09:31:05: 12000000 INFO @ Tue, 14 Jul 2020 09:31:09: 24000000 INFO @ Tue, 14 Jul 2020 09:31:10: 19000000 INFO @ Tue, 14 Jul 2020 09:31:12: 13000000 INFO @ Tue, 14 Jul 2020 09:31:16: 25000000 INFO @ Tue, 14 Jul 2020 09:31:17: 20000000 INFO @ Tue, 14 Jul 2020 09:31:20: 14000000 INFO @ Tue, 14 Jul 2020 09:31:22: 26000000 INFO @ Tue, 14 Jul 2020 09:31:23: 21000000 INFO @ Tue, 14 Jul 2020 09:31:27: 15000000 INFO @ Tue, 14 Jul 2020 09:31:29: 27000000 INFO @ Tue, 14 Jul 2020 09:31:29: 22000000 INFO @ Tue, 14 Jul 2020 09:31:34: 16000000 INFO @ Tue, 14 Jul 2020 09:31:35: 28000000 INFO @ Tue, 14 Jul 2020 09:31:36: 23000000 INFO @ Tue, 14 Jul 2020 09:31:41: 17000000 INFO @ Tue, 14 Jul 2020 09:31:42: 29000000 INFO @ Tue, 14 Jul 2020 09:31:42: 24000000 INFO @ Tue, 14 Jul 2020 09:31:48: 30000000 INFO @ Tue, 14 Jul 2020 09:31:49: 25000000 INFO @ Tue, 14 Jul 2020 09:31:49: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:31:55: 31000000 INFO @ Tue, 14 Jul 2020 09:31:55: 26000000 INFO @ Tue, 14 Jul 2020 09:31:56: 19000000 INFO @ Tue, 14 Jul 2020 09:32:01: 32000000 INFO @ Tue, 14 Jul 2020 09:32:01: 27000000 INFO @ Tue, 14 Jul 2020 09:32:03: 20000000 INFO @ Tue, 14 Jul 2020 09:32:04: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 09:32:04: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 09:32:04: #1 total tags in treatment: 15189602 INFO @ Tue, 14 Jul 2020 09:32:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:32:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:32:04: #1 tags after filtering in treatment: 12699036 INFO @ Tue, 14 Jul 2020 09:32:04: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 14 Jul 2020 09:32:04: #1 finished! INFO @ Tue, 14 Jul 2020 09:32:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:32:05: #2 number of paired peaks: 5086 INFO @ Tue, 14 Jul 2020 09:32:05: start model_add_line... INFO @ Tue, 14 Jul 2020 09:32:05: start X-correlation... INFO @ Tue, 14 Jul 2020 09:32:05: end of X-cor INFO @ Tue, 14 Jul 2020 09:32:05: #2 finished! INFO @ Tue, 14 Jul 2020 09:32:05: #2 predicted fragment length is 180 bps INFO @ Tue, 14 Jul 2020 09:32:05: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 14 Jul 2020 09:32:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.05_model.r INFO @ Tue, 14 Jul 2020 09:32:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:32:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:32:08: 28000000 INFO @ Tue, 14 Jul 2020 09:32:11: 21000000 INFO @ Tue, 14 Jul 2020 09:32:14: 29000000 INFO @ Tue, 14 Jul 2020 09:32:18: 22000000 INFO @ Tue, 14 Jul 2020 09:32:21: 30000000 INFO @ Tue, 14 Jul 2020 09:32:25: 23000000 INFO @ Tue, 14 Jul 2020 09:32:27: 31000000 INFO @ Tue, 14 Jul 2020 09:32:32: 24000000 INFO @ Tue, 14 Jul 2020 09:32:34: 32000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:32:36: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 09:32:36: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 09:32:36: #1 total tags in treatment: 15189602 INFO @ Tue, 14 Jul 2020 09:32:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:32:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:32:36: #1 tags after filtering in treatment: 12699036 INFO @ Tue, 14 Jul 2020 09:32:36: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 14 Jul 2020 09:32:36: #1 finished! INFO @ Tue, 14 Jul 2020 09:32:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:32:37: #2 number of paired peaks: 5086 INFO @ Tue, 14 Jul 2020 09:32:37: start model_add_line... INFO @ Tue, 14 Jul 2020 09:32:38: start X-correlation... INFO @ Tue, 14 Jul 2020 09:32:38: end of X-cor INFO @ Tue, 14 Jul 2020 09:32:38: #2 finished! INFO @ Tue, 14 Jul 2020 09:32:38: #2 predicted fragment length is 180 bps INFO @ Tue, 14 Jul 2020 09:32:38: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 14 Jul 2020 09:32:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.10_model.r INFO @ Tue, 14 Jul 2020 09:32:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:32:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:32:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:32:39: 25000000 INFO @ Tue, 14 Jul 2020 09:32:46: 26000000 INFO @ Tue, 14 Jul 2020 09:32:52: 27000000 INFO @ Tue, 14 Jul 2020 09:32:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.05_summits.bed INFO @ Tue, 14 Jul 2020 09:32:54: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14267 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:32:59: 28000000 INFO @ Tue, 14 Jul 2020 09:33:06: 29000000 INFO @ Tue, 14 Jul 2020 09:33:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:33:12: 30000000 INFO @ Tue, 14 Jul 2020 09:33:18: 31000000 INFO @ Tue, 14 Jul 2020 09:33:25: 32000000 INFO @ Tue, 14 Jul 2020 09:33:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:33:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:33:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.10_summits.bed INFO @ Tue, 14 Jul 2020 09:33:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9065 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:33:27: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 09:33:27: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 09:33:27: #1 total tags in treatment: 15189602 INFO @ Tue, 14 Jul 2020 09:33:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:33:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:33:27: #1 tags after filtering in treatment: 12699036 INFO @ Tue, 14 Jul 2020 09:33:27: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 14 Jul 2020 09:33:27: #1 finished! INFO @ Tue, 14 Jul 2020 09:33:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:33:28: #2 number of paired peaks: 5086 INFO @ Tue, 14 Jul 2020 09:33:28: start model_add_line... INFO @ Tue, 14 Jul 2020 09:33:28: start X-correlation... INFO @ Tue, 14 Jul 2020 09:33:28: end of X-cor INFO @ Tue, 14 Jul 2020 09:33:28: #2 finished! INFO @ Tue, 14 Jul 2020 09:33:28: #2 predicted fragment length is 180 bps INFO @ Tue, 14 Jul 2020 09:33:28: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 14 Jul 2020 09:33:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.20_model.r INFO @ Tue, 14 Jul 2020 09:33:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:33:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:34:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:34:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:34:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:34:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224526/SRX7224526.20_summits.bed INFO @ Tue, 14 Jul 2020 09:34:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4652 records, 4 fields): 6 millis CompletedMACS2peakCalling