Job ID = 6626558 SRX = SRX7224528 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19420322 spots for SRR10541176/SRR10541176.sra Written 19420322 spots for SRR10541176/SRR10541176.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627113 ("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: 01:40:04 19420322 reads; of these: 19420322 (100.00%) were paired; of these: 2197442 (11.32%) aligned concordantly 0 times 5817001 (29.95%) aligned concordantly exactly 1 time 11405879 (58.73%) aligned concordantly >1 times ---- 2197442 pairs aligned concordantly 0 times; of these: 51492 (2.34%) aligned discordantly 1 time ---- 2145950 pairs aligned 0 times concordantly or discordantly; of these: 4291900 mates make up the pairs; of these: 2116408 (49.31%) aligned 0 times 366023 (8.53%) aligned exactly 1 time 1809469 (42.16%) aligned >1 times 94.55% overall alignment rate Time searching: 01:40:04 Overall time: 01:40:04 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] 873845 / 17221900 = 0.0507 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 09:23:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.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 09:23:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:23:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:23:49: 1000000 INFO @ Tue, 14 Jul 2020 09:23:55: 2000000 INFO @ Tue, 14 Jul 2020 09:24:00: 3000000 INFO @ Tue, 14 Jul 2020 09:24:06: 4000000 INFO @ Tue, 14 Jul 2020 09:24:11: 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 09:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.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 09:24:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:24:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:24:17: 6000000 INFO @ Tue, 14 Jul 2020 09:24:20: 1000000 INFO @ Tue, 14 Jul 2020 09:24:23: 7000000 INFO @ Tue, 14 Jul 2020 09:24:26: 2000000 INFO @ Tue, 14 Jul 2020 09:24:29: 8000000 INFO @ Tue, 14 Jul 2020 09:24:33: 3000000 INFO @ Tue, 14 Jul 2020 09:24:36: 9000000 INFO @ Tue, 14 Jul 2020 09:24:39: 4000000 BedGraph に変換中... INFO @ Tue, 14 Jul 2020 09:24:42: 10000000 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 09:24:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.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 09:24:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:24:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:24:45: 5000000 INFO @ Tue, 14 Jul 2020 09:24:48: 11000000 INFO @ Tue, 14 Jul 2020 09:24:50: 1000000 INFO @ Tue, 14 Jul 2020 09:24:51: 6000000 INFO @ Tue, 14 Jul 2020 09:24:55: 12000000 INFO @ Tue, 14 Jul 2020 09:24:57: 2000000 INFO @ Tue, 14 Jul 2020 09:24:58: 7000000 INFO @ Tue, 14 Jul 2020 09:25:01: 13000000 INFO @ Tue, 14 Jul 2020 09:25:03: 3000000 INFO @ Tue, 14 Jul 2020 09:25:04: 8000000 INFO @ Tue, 14 Jul 2020 09:25:07: 14000000 INFO @ Tue, 14 Jul 2020 09:25:09: 4000000 INFO @ Tue, 14 Jul 2020 09:25:10: 9000000 INFO @ Tue, 14 Jul 2020 09:25:14: 15000000 INFO @ Tue, 14 Jul 2020 09:25:16: 5000000 INFO @ Tue, 14 Jul 2020 09:25:17: 10000000 INFO @ Tue, 14 Jul 2020 09:25:20: 16000000 INFO @ Tue, 14 Jul 2020 09:25:22: 6000000 INFO @ Tue, 14 Jul 2020 09:25:23: 11000000 INFO @ Tue, 14 Jul 2020 09:25:26: 17000000 INFO @ Tue, 14 Jul 2020 09:25:28: 7000000 INFO @ Tue, 14 Jul 2020 09:25:30: 12000000 INFO @ Tue, 14 Jul 2020 09:25:32: 18000000 INFO @ Tue, 14 Jul 2020 09:25:35: 8000000 INFO @ Tue, 14 Jul 2020 09:25:36: 13000000 INFO @ Tue, 14 Jul 2020 09:25:39: 19000000 INFO @ Tue, 14 Jul 2020 09:25:41: 9000000 INFO @ Tue, 14 Jul 2020 09:25:43: 14000000 INFO @ Tue, 14 Jul 2020 09:25:45: 20000000 INFO @ Tue, 14 Jul 2020 09:25:47: 10000000 INFO @ Tue, 14 Jul 2020 09:25:49: 15000000 INFO @ Tue, 14 Jul 2020 09:25:51: 21000000 INFO @ Tue, 14 Jul 2020 09:25:54: 11000000 INFO @ Tue, 14 Jul 2020 09:25:55: 16000000 INFO @ Tue, 14 Jul 2020 09:25:58: 22000000 INFO @ Tue, 14 Jul 2020 09:26:00: 12000000 INFO @ Tue, 14 Jul 2020 09:26:02: 17000000 INFO @ Tue, 14 Jul 2020 09:26:04: 23000000 INFO @ Tue, 14 Jul 2020 09:26:06: 13000000 INFO @ Tue, 14 Jul 2020 09:26:08: 18000000 INFO @ Tue, 14 Jul 2020 09:26:10: 24000000 INFO @ Tue, 14 Jul 2020 09:26:13: 14000000 INFO @ Tue, 14 Jul 2020 09:26:14: 19000000 INFO @ Tue, 14 Jul 2020 09:26:17: 25000000 INFO @ Tue, 14 Jul 2020 09:26:19: 15000000 INFO @ Tue, 14 Jul 2020 09:26:21: 20000000 INFO @ Tue, 14 Jul 2020 09:26:23: 26000000 INFO @ Tue, 14 Jul 2020 09:26:25: 16000000 INFO @ Tue, 14 Jul 2020 09:26:27: 21000000 INFO @ Tue, 14 Jul 2020 09:26:29: 27000000 INFO @ Tue, 14 Jul 2020 09:26:32: 17000000 INFO @ Tue, 14 Jul 2020 09:26:33: 22000000 INFO @ Tue, 14 Jul 2020 09:26:36: 28000000 INFO @ Tue, 14 Jul 2020 09:26:38: 18000000 INFO @ Tue, 14 Jul 2020 09:26:40: 23000000 INFO @ Tue, 14 Jul 2020 09:26:42: 29000000 INFO @ Tue, 14 Jul 2020 09:26:44: 19000000 INFO @ Tue, 14 Jul 2020 09:26:46: 24000000 INFO @ Tue, 14 Jul 2020 09:26:48: 30000000 INFO @ Tue, 14 Jul 2020 09:26:51: 20000000 INFO @ Tue, 14 Jul 2020 09:26:52: 25000000 INFO @ Tue, 14 Jul 2020 09:26:55: 31000000 INFO @ Tue, 14 Jul 2020 09:26:57: 21000000 INFO @ Tue, 14 Jul 2020 09:26:59: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:27:01: 32000000 INFO @ Tue, 14 Jul 2020 09:27:03: 22000000 INFO @ Tue, 14 Jul 2020 09:27:05: 27000000 INFO @ Tue, 14 Jul 2020 09:27:07: 33000000 INFO @ Tue, 14 Jul 2020 09:27:10: 23000000 INFO @ Tue, 14 Jul 2020 09:27:11: 28000000 INFO @ Tue, 14 Jul 2020 09:27:14: 34000000 INFO @ Tue, 14 Jul 2020 09:27:16: 24000000 INFO @ Tue, 14 Jul 2020 09:27:18: 29000000 INFO @ Tue, 14 Jul 2020 09:27:20: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 09:27:20: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 09:27:20: #1 total tags in treatment: 16349738 INFO @ Tue, 14 Jul 2020 09:27:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:27:20: #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 09:27:20: #1 tags after filtering in treatment: 13981969 INFO @ Tue, 14 Jul 2020 09:27:20: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 14 Jul 2020 09:27:20: #1 finished! INFO @ Tue, 14 Jul 2020 09:27:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:27:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:27:21: #2 number of paired peaks: 4335 INFO @ Tue, 14 Jul 2020 09:27:21: start model_add_line... INFO @ Tue, 14 Jul 2020 09:27:22: start X-correlation... INFO @ Tue, 14 Jul 2020 09:27:22: end of X-cor INFO @ Tue, 14 Jul 2020 09:27:22: #2 finished! INFO @ Tue, 14 Jul 2020 09:27:22: #2 predicted fragment length is 184 bps INFO @ Tue, 14 Jul 2020 09:27:22: #2 alternative fragment length(s) may be 4,184 bps INFO @ Tue, 14 Jul 2020 09:27:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.05_model.r INFO @ Tue, 14 Jul 2020 09:27:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:27:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:27:22: 25000000 INFO @ Tue, 14 Jul 2020 09:27:24: 30000000 INFO @ Tue, 14 Jul 2020 09:27:28: 26000000 INFO @ Tue, 14 Jul 2020 09:27:30: 31000000 INFO @ Tue, 14 Jul 2020 09:27:35: 27000000 INFO @ Tue, 14 Jul 2020 09:27:36: 32000000 INFO @ Tue, 14 Jul 2020 09:27:41: 28000000 INFO @ Tue, 14 Jul 2020 09:27:43: 33000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:27:47: 29000000 INFO @ Tue, 14 Jul 2020 09:27:49: 34000000 INFO @ Tue, 14 Jul 2020 09:27:53: 30000000 INFO @ Tue, 14 Jul 2020 09:27:55: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 09:27:55: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 09:27:55: #1 total tags in treatment: 16349738 INFO @ Tue, 14 Jul 2020 09:27:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:27:55: #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 09:27:55: #1 tags after filtering in treatment: 13981969 INFO @ Tue, 14 Jul 2020 09:27:55: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 14 Jul 2020 09:27:55: #1 finished! INFO @ Tue, 14 Jul 2020 09:27:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:27:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:27:56: #2 number of paired peaks: 4335 INFO @ Tue, 14 Jul 2020 09:27:56: start model_add_line... INFO @ Tue, 14 Jul 2020 09:27:57: start X-correlation... INFO @ Tue, 14 Jul 2020 09:27:57: end of X-cor INFO @ Tue, 14 Jul 2020 09:27:57: #2 finished! INFO @ Tue, 14 Jul 2020 09:27:57: #2 predicted fragment length is 184 bps INFO @ Tue, 14 Jul 2020 09:27:57: #2 alternative fragment length(s) may be 4,184 bps INFO @ Tue, 14 Jul 2020 09:27:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.10_model.r INFO @ Tue, 14 Jul 2020 09:27:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:27:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:27:59: 31000000 INFO @ Tue, 14 Jul 2020 09:28:05: 32000000 INFO @ Tue, 14 Jul 2020 09:28:11: 33000000 INFO @ Tue, 14 Jul 2020 09:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.05_summits.bed INFO @ Tue, 14 Jul 2020 09:28:12: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14213 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:28:17: 34000000 INFO @ Tue, 14 Jul 2020 09:28:23: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 09:28:23: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 09:28:23: #1 total tags in treatment: 16349738 INFO @ Tue, 14 Jul 2020 09:28:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:28:23: #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 09:28:23: #1 tags after filtering in treatment: 13981969 INFO @ Tue, 14 Jul 2020 09:28:23: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 14 Jul 2020 09:28:23: #1 finished! INFO @ Tue, 14 Jul 2020 09:28:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:28:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:28:24: #2 number of paired peaks: 4335 INFO @ Tue, 14 Jul 2020 09:28:24: start model_add_line... INFO @ Tue, 14 Jul 2020 09:28:24: start X-correlation... INFO @ Tue, 14 Jul 2020 09:28:24: end of X-cor INFO @ Tue, 14 Jul 2020 09:28:24: #2 finished! INFO @ Tue, 14 Jul 2020 09:28:24: #2 predicted fragment length is 184 bps INFO @ Tue, 14 Jul 2020 09:28:24: #2 alternative fragment length(s) may be 4,184 bps INFO @ Tue, 14 Jul 2020 09:28:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.20_model.r INFO @ Tue, 14 Jul 2020 09:28:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:28:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:28:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.10_summits.bed INFO @ Tue, 14 Jul 2020 09:28:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9095 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:29:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:29:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:29:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:29:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224528/SRX7224528.20_summits.bed INFO @ Tue, 14 Jul 2020 09:29:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4356 records, 4 fields): 13 millis CompletedMACS2peakCalling