Job ID = 14160443 SRX = SRX8582578 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15040156 spots for SRR12054156/SRR12054156.sra Written 15040156 spots for SRR12054156/SRR12054156.sra Read 14921934 spots for SRR12054157/SRR12054157.sra Written 14921934 spots for SRR12054157/SRR12054157.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160656 ("srTce11") 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: 00:31:16 29962090 reads; of these: 29962090 (100.00%) were paired; of these: 4024277 (13.43%) aligned concordantly 0 times 22466496 (74.98%) aligned concordantly exactly 1 time 3471317 (11.59%) aligned concordantly >1 times ---- 4024277 pairs aligned concordantly 0 times; of these: 2110706 (52.45%) aligned discordantly 1 time ---- 1913571 pairs aligned 0 times concordantly or discordantly; of these: 3827142 mates make up the pairs; of these: 2398241 (62.66%) aligned 0 times 848805 (22.18%) aligned exactly 1 time 580096 (15.16%) aligned >1 times 96.00% overall alignment rate Time searching: 00:31:16 Overall time: 00:31:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 24 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 7756760 / 28036554 = 0.2767 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:22:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 09 Dec 2021 03:22:20: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:22:20: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:22:29: 1000000 INFO @ Thu, 09 Dec 2021 03:22:37: 2000000 INFO @ Thu, 09 Dec 2021 03:22:46: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:22:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 09 Dec 2021 03:22:50: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:22:50: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:22:54: 4000000 INFO @ Thu, 09 Dec 2021 03:22:58: 1000000 INFO @ Thu, 09 Dec 2021 03:23:03: 5000000 INFO @ Thu, 09 Dec 2021 03:23:06: 2000000 INFO @ Thu, 09 Dec 2021 03:23:11: 6000000 INFO @ Thu, 09 Dec 2021 03:23:13: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 09 Dec 2021 03:23:20: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:23:20: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:23:20: 7000000 INFO @ Thu, 09 Dec 2021 03:23:20: 4000000 INFO @ Thu, 09 Dec 2021 03:23:28: 5000000 INFO @ Thu, 09 Dec 2021 03:23:28: 1000000 INFO @ Thu, 09 Dec 2021 03:23:29: 8000000 INFO @ Thu, 09 Dec 2021 03:23:36: 6000000 INFO @ Thu, 09 Dec 2021 03:23:36: 2000000 INFO @ Thu, 09 Dec 2021 03:23:38: 9000000 INFO @ Thu, 09 Dec 2021 03:23:43: 7000000 INFO @ Thu, 09 Dec 2021 03:23:44: 3000000 INFO @ Thu, 09 Dec 2021 03:23:47: 10000000 INFO @ Thu, 09 Dec 2021 03:23:51: 8000000 INFO @ Thu, 09 Dec 2021 03:23:52: 4000000 INFO @ Thu, 09 Dec 2021 03:23:55: 11000000 INFO @ Thu, 09 Dec 2021 03:24:00: 9000000 INFO @ Thu, 09 Dec 2021 03:24:00: 5000000 INFO @ Thu, 09 Dec 2021 03:24:04: 12000000 INFO @ Thu, 09 Dec 2021 03:24:08: 10000000 INFO @ Thu, 09 Dec 2021 03:24:08: 6000000 INFO @ Thu, 09 Dec 2021 03:24:13: 13000000 INFO @ Thu, 09 Dec 2021 03:24:16: 11000000 INFO @ Thu, 09 Dec 2021 03:24:16: 7000000 INFO @ Thu, 09 Dec 2021 03:24:22: 14000000 INFO @ Thu, 09 Dec 2021 03:24:24: 12000000 INFO @ Thu, 09 Dec 2021 03:24:24: 8000000 INFO @ Thu, 09 Dec 2021 03:24:30: 15000000 INFO @ Thu, 09 Dec 2021 03:24:33: 13000000 INFO @ Thu, 09 Dec 2021 03:24:33: 9000000 INFO @ Thu, 09 Dec 2021 03:24:39: 16000000 INFO @ Thu, 09 Dec 2021 03:24:42: 14000000 INFO @ Thu, 09 Dec 2021 03:24:42: 10000000 INFO @ Thu, 09 Dec 2021 03:24:48: 17000000 INFO @ Thu, 09 Dec 2021 03:24:50: 11000000 INFO @ Thu, 09 Dec 2021 03:24:50: 15000000 INFO @ Thu, 09 Dec 2021 03:24:57: 18000000 INFO @ Thu, 09 Dec 2021 03:24:59: 12000000 INFO @ Thu, 09 Dec 2021 03:24:59: 16000000 INFO @ Thu, 09 Dec 2021 03:25:05: 19000000 INFO @ Thu, 09 Dec 2021 03:25:07: 13000000 INFO @ Thu, 09 Dec 2021 03:25:07: 17000000 INFO @ Thu, 09 Dec 2021 03:25:13: 20000000 INFO @ Thu, 09 Dec 2021 03:25:16: 14000000 INFO @ Thu, 09 Dec 2021 03:25:16: 18000000 INFO @ Thu, 09 Dec 2021 03:25:22: 21000000 INFO @ Thu, 09 Dec 2021 03:25:24: 19000000 INFO @ Thu, 09 Dec 2021 03:25:24: 15000000 INFO @ Thu, 09 Dec 2021 03:25:30: 22000000 INFO @ Thu, 09 Dec 2021 03:25:32: 20000000 INFO @ Thu, 09 Dec 2021 03:25:32: 16000000 INFO @ Thu, 09 Dec 2021 03:25:38: 23000000 INFO @ Thu, 09 Dec 2021 03:25:41: 21000000 INFO @ Thu, 09 Dec 2021 03:25:41: 17000000 INFO @ Thu, 09 Dec 2021 03:25:46: 24000000 INFO @ Thu, 09 Dec 2021 03:25:49: 22000000 INFO @ Thu, 09 Dec 2021 03:25:49: 18000000 INFO @ Thu, 09 Dec 2021 03:25:55: 25000000 INFO @ Thu, 09 Dec 2021 03:25:57: 23000000 INFO @ Thu, 09 Dec 2021 03:25:58: 19000000 INFO @ Thu, 09 Dec 2021 03:26:03: 26000000 INFO @ Thu, 09 Dec 2021 03:26:06: 24000000 INFO @ Thu, 09 Dec 2021 03:26:06: 20000000 INFO @ Thu, 09 Dec 2021 03:26:11: 27000000 INFO @ Thu, 09 Dec 2021 03:26:13: 25000000 INFO @ Thu, 09 Dec 2021 03:26:13: 21000000 INFO @ Thu, 09 Dec 2021 03:26:19: 28000000 INFO @ Thu, 09 Dec 2021 03:26:20: 26000000 INFO @ Thu, 09 Dec 2021 03:26:20: 22000000 INFO @ Thu, 09 Dec 2021 03:26:27: 29000000 INFO @ Thu, 09 Dec 2021 03:26:27: 27000000 INFO @ Thu, 09 Dec 2021 03:26:28: 23000000 INFO @ Thu, 09 Dec 2021 03:26:34: 28000000 INFO @ Thu, 09 Dec 2021 03:26:35: 24000000 INFO @ Thu, 09 Dec 2021 03:26:35: 30000000 INFO @ Thu, 09 Dec 2021 03:26:42: 29000000 INFO @ Thu, 09 Dec 2021 03:26:42: 25000000 INFO @ Thu, 09 Dec 2021 03:26:43: 31000000 INFO @ Thu, 09 Dec 2021 03:26:49: 30000000 INFO @ Thu, 09 Dec 2021 03:26:49: 26000000 INFO @ Thu, 09 Dec 2021 03:26:51: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:26:56: 31000000 INFO @ Thu, 09 Dec 2021 03:26:56: 27000000 INFO @ Thu, 09 Dec 2021 03:26:59: 33000000 INFO @ Thu, 09 Dec 2021 03:27:03: 32000000 INFO @ Thu, 09 Dec 2021 03:27:03: 28000000 INFO @ Thu, 09 Dec 2021 03:27:07: 34000000 INFO @ Thu, 09 Dec 2021 03:27:10: 33000000 INFO @ Thu, 09 Dec 2021 03:27:11: 29000000 INFO @ Thu, 09 Dec 2021 03:27:16: 35000000 INFO @ Thu, 09 Dec 2021 03:27:17: 34000000 INFO @ Thu, 09 Dec 2021 03:27:18: 30000000 INFO @ Thu, 09 Dec 2021 03:27:24: 36000000 INFO @ Thu, 09 Dec 2021 03:27:24: 35000000 INFO @ Thu, 09 Dec 2021 03:27:25: 31000000 INFO @ Thu, 09 Dec 2021 03:27:32: 36000000 INFO @ Thu, 09 Dec 2021 03:27:32: 32000000 INFO @ Thu, 09 Dec 2021 03:27:33: 37000000 INFO @ Thu, 09 Dec 2021 03:27:39: 37000000 INFO @ Thu, 09 Dec 2021 03:27:40: 33000000 INFO @ Thu, 09 Dec 2021 03:27:41: 38000000 INFO @ Thu, 09 Dec 2021 03:27:46: 38000000 INFO @ Thu, 09 Dec 2021 03:27:47: 34000000 INFO @ Thu, 09 Dec 2021 03:27:49: 39000000 INFO @ Thu, 09 Dec 2021 03:27:54: 39000000 INFO @ Thu, 09 Dec 2021 03:27:54: 35000000 INFO @ Thu, 09 Dec 2021 03:27:58: 40000000 INFO @ Thu, 09 Dec 2021 03:28:01: 40000000 INFO @ Thu, 09 Dec 2021 03:28:01: 36000000 INFO @ Thu, 09 Dec 2021 03:28:06: 41000000 INFO @ Thu, 09 Dec 2021 03:28:08: 41000000 INFO @ Thu, 09 Dec 2021 03:28:09: 37000000 INFO @ Thu, 09 Dec 2021 03:28:14: 42000000 INFO @ Thu, 09 Dec 2021 03:28:14: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:28:14: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:28:14: #1 total tags in treatment: 18568403 INFO @ Thu, 09 Dec 2021 03:28:14: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:28:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:28:15: #1 tags after filtering in treatment: 16209192 INFO @ Thu, 09 Dec 2021 03:28:15: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 03:28:15: #1 finished! INFO @ Thu, 09 Dec 2021 03:28:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:28:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:28:15: 42000000 INFO @ Thu, 09 Dec 2021 03:28:15: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:28:15: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:28:15: #1 total tags in treatment: 18568403 INFO @ Thu, 09 Dec 2021 03:28:15: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:28:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:28:16: #1 tags after filtering in treatment: 16209192 INFO @ Thu, 09 Dec 2021 03:28:16: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 03:28:16: #1 finished! INFO @ Thu, 09 Dec 2021 03:28:16: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:28:16: 38000000 INFO @ Thu, 09 Dec 2021 03:28:16: #2 number of paired peaks: 529 WARNING @ Thu, 09 Dec 2021 03:28:16: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Thu, 09 Dec 2021 03:28:16: start model_add_line... INFO @ Thu, 09 Dec 2021 03:28:16: start X-correlation... INFO @ Thu, 09 Dec 2021 03:28:16: end of X-cor INFO @ Thu, 09 Dec 2021 03:28:16: #2 finished! INFO @ Thu, 09 Dec 2021 03:28:16: #2 predicted fragment length is 210 bps INFO @ Thu, 09 Dec 2021 03:28:16: #2 alternative fragment length(s) may be 210 bps INFO @ Thu, 09 Dec 2021 03:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.05_model.r INFO @ Thu, 09 Dec 2021 03:28:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:28:17: #2 number of paired peaks: 529 WARNING @ Thu, 09 Dec 2021 03:28:17: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Thu, 09 Dec 2021 03:28:17: start model_add_line... INFO @ Thu, 09 Dec 2021 03:28:17: start X-correlation... INFO @ Thu, 09 Dec 2021 03:28:17: end of X-cor INFO @ Thu, 09 Dec 2021 03:28:17: #2 finished! INFO @ Thu, 09 Dec 2021 03:28:17: #2 predicted fragment length is 210 bps INFO @ Thu, 09 Dec 2021 03:28:17: #2 alternative fragment length(s) may be 210 bps INFO @ Thu, 09 Dec 2021 03:28:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.10_model.r INFO @ Thu, 09 Dec 2021 03:28:17: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:28:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:28:23: 39000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:28:29: 40000000 INFO @ Thu, 09 Dec 2021 03:28:36: 41000000 INFO @ Thu, 09 Dec 2021 03:28:43: 42000000 INFO @ Thu, 09 Dec 2021 03:28:43: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:28:43: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:28:43: #1 total tags in treatment: 18568403 INFO @ Thu, 09 Dec 2021 03:28:43: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:28:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:28:44: #1 tags after filtering in treatment: 16209192 INFO @ Thu, 09 Dec 2021 03:28:44: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 03:28:44: #1 finished! INFO @ Thu, 09 Dec 2021 03:28:44: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:28:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:28:45: #2 number of paired peaks: 529 WARNING @ Thu, 09 Dec 2021 03:28:45: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Thu, 09 Dec 2021 03:28:45: start model_add_line... INFO @ Thu, 09 Dec 2021 03:28:45: start X-correlation... INFO @ Thu, 09 Dec 2021 03:28:45: end of X-cor INFO @ Thu, 09 Dec 2021 03:28:45: #2 finished! INFO @ Thu, 09 Dec 2021 03:28:45: #2 predicted fragment length is 210 bps INFO @ Thu, 09 Dec 2021 03:28:45: #2 alternative fragment length(s) may be 210 bps INFO @ Thu, 09 Dec 2021 03:28:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.20_model.r INFO @ Thu, 09 Dec 2021 03:28:45: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:28:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:29:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:29:06: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:29:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.10_summits.bed INFO @ Thu, 09 Dec 2021 03:29:26: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6408 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:29:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.05_summits.bed INFO @ Thu, 09 Dec 2021 03:29:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9241 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:29:33: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:29:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8582578/SRX8582578.20_summits.bed INFO @ Thu, 09 Dec 2021 03:29:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3552 records, 4 fields): 11 millis CompletedMACS2peakCalling