Job ID = 6368461 SRX = SRX4996818 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:13:50 prefetch.2.10.7: 1) Downloading 'SRR8176703'... 2020-06-16T00:13:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:53 prefetch.2.10.7: 1) 'SRR8176703' was downloaded successfully 2020-06-16T00:16:53 prefetch.2.10.7: 'SRR8176703' has 0 unresolved dependencies Read 18953288 spots for SRR8176703/SRR8176703.sra Written 18953288 spots for SRR8176703/SRR8176703.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:01 18953288 reads; of these: 18953288 (100.00%) were paired; of these: 2421177 (12.77%) aligned concordantly 0 times 14046109 (74.11%) aligned concordantly exactly 1 time 2486002 (13.12%) aligned concordantly >1 times ---- 2421177 pairs aligned concordantly 0 times; of these: 1632197 (67.41%) aligned discordantly 1 time ---- 788980 pairs aligned 0 times concordantly or discordantly; of these: 1577960 mates make up the pairs; of these: 712629 (45.16%) aligned 0 times 436999 (27.69%) aligned exactly 1 time 428332 (27.14%) aligned >1 times 98.12% overall alignment rate Time searching: 00:17:01 Overall time: 00:17:01 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 16 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] 284382 / 18149933 = 0.0157 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, 16 Jun 2020 09:44:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.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 @ Tue, 16 Jun 2020 09:44:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:53: 1000000 INFO @ Tue, 16 Jun 2020 09:44:58: 2000000 INFO @ Tue, 16 Jun 2020 09:45:03: 3000000 INFO @ Tue, 16 Jun 2020 09:45:08: 4000000 INFO @ Tue, 16 Jun 2020 09:45:13: 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, 16 Jun 2020 09:45:18: 6000000 INFO @ Tue, 16 Jun 2020 09:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.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 @ Tue, 16 Jun 2020 09:45:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:24: 7000000 INFO @ Tue, 16 Jun 2020 09:45:25: 1000000 INFO @ Tue, 16 Jun 2020 09:45:30: 8000000 INFO @ Tue, 16 Jun 2020 09:45:32: 2000000 INFO @ Tue, 16 Jun 2020 09:45:36: 9000000 INFO @ Tue, 16 Jun 2020 09:45:39: 3000000 INFO @ Tue, 16 Jun 2020 09:45:42: 10000000 INFO @ Tue, 16 Jun 2020 09:45:45: 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, 16 Jun 2020 09:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.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 @ Tue, 16 Jun 2020 09:45:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:48: 11000000 INFO @ Tue, 16 Jun 2020 09:45:52: 5000000 INFO @ Tue, 16 Jun 2020 09:45:54: 12000000 INFO @ Tue, 16 Jun 2020 09:45:55: 1000000 INFO @ Tue, 16 Jun 2020 09:45:59: 6000000 INFO @ Tue, 16 Jun 2020 09:46:00: 13000000 INFO @ Tue, 16 Jun 2020 09:46:02: 2000000 INFO @ Tue, 16 Jun 2020 09:46:06: 7000000 INFO @ Tue, 16 Jun 2020 09:46:06: 14000000 INFO @ Tue, 16 Jun 2020 09:46:09: 3000000 INFO @ Tue, 16 Jun 2020 09:46:13: 15000000 INFO @ Tue, 16 Jun 2020 09:46:13: 8000000 INFO @ Tue, 16 Jun 2020 09:46:16: 4000000 INFO @ Tue, 16 Jun 2020 09:46:19: 16000000 INFO @ Tue, 16 Jun 2020 09:46:20: 9000000 INFO @ Tue, 16 Jun 2020 09:46:23: 5000000 INFO @ Tue, 16 Jun 2020 09:46:25: 17000000 INFO @ Tue, 16 Jun 2020 09:46:27: 10000000 INFO @ Tue, 16 Jun 2020 09:46:29: 6000000 INFO @ Tue, 16 Jun 2020 09:46:31: 18000000 INFO @ Tue, 16 Jun 2020 09:46:34: 11000000 INFO @ Tue, 16 Jun 2020 09:46:36: 7000000 INFO @ Tue, 16 Jun 2020 09:46:37: 19000000 INFO @ Tue, 16 Jun 2020 09:46:41: 12000000 INFO @ Tue, 16 Jun 2020 09:46:43: 20000000 INFO @ Tue, 16 Jun 2020 09:46:43: 8000000 INFO @ Tue, 16 Jun 2020 09:46:48: 13000000 INFO @ Tue, 16 Jun 2020 09:46:49: 21000000 INFO @ Tue, 16 Jun 2020 09:46:50: 9000000 INFO @ Tue, 16 Jun 2020 09:46:55: 14000000 INFO @ Tue, 16 Jun 2020 09:46:55: 22000000 INFO @ Tue, 16 Jun 2020 09:46:57: 10000000 INFO @ Tue, 16 Jun 2020 09:47:01: 23000000 INFO @ Tue, 16 Jun 2020 09:47:02: 15000000 INFO @ Tue, 16 Jun 2020 09:47:04: 11000000 INFO @ Tue, 16 Jun 2020 09:47:07: 24000000 INFO @ Tue, 16 Jun 2020 09:47:09: 16000000 INFO @ Tue, 16 Jun 2020 09:47:11: 12000000 INFO @ Tue, 16 Jun 2020 09:47:13: 25000000 INFO @ Tue, 16 Jun 2020 09:47:15: 17000000 INFO @ Tue, 16 Jun 2020 09:47:18: 13000000 INFO @ Tue, 16 Jun 2020 09:47:19: 26000000 INFO @ Tue, 16 Jun 2020 09:47:22: 18000000 INFO @ Tue, 16 Jun 2020 09:47:25: 14000000 INFO @ Tue, 16 Jun 2020 09:47:25: 27000000 INFO @ Tue, 16 Jun 2020 09:47:29: 19000000 INFO @ Tue, 16 Jun 2020 09:47:31: 28000000 INFO @ Tue, 16 Jun 2020 09:47:32: 15000000 INFO @ Tue, 16 Jun 2020 09:47:36: 20000000 INFO @ Tue, 16 Jun 2020 09:47:38: 29000000 INFO @ Tue, 16 Jun 2020 09:47:39: 16000000 INFO @ Tue, 16 Jun 2020 09:47:44: 21000000 INFO @ Tue, 16 Jun 2020 09:47:44: 30000000 INFO @ Tue, 16 Jun 2020 09:47:46: 17000000 INFO @ Tue, 16 Jun 2020 09:47:50: 31000000 INFO @ Tue, 16 Jun 2020 09:47:51: 22000000 INFO @ Tue, 16 Jun 2020 09:47:53: 18000000 INFO @ Tue, 16 Jun 2020 09:47:56: 32000000 INFO @ Tue, 16 Jun 2020 09:47:57: 23000000 INFO @ Tue, 16 Jun 2020 09:48:00: 19000000 INFO @ Tue, 16 Jun 2020 09:48:02: 33000000 INFO @ Tue, 16 Jun 2020 09:48:04: 24000000 INFO @ Tue, 16 Jun 2020 09:48:07: 20000000 INFO @ Tue, 16 Jun 2020 09:48:08: 34000000 INFO @ Tue, 16 Jun 2020 09:48:11: 25000000 INFO @ Tue, 16 Jun 2020 09:48:14: 21000000 INFO @ Tue, 16 Jun 2020 09:48:14: 35000000 INFO @ Tue, 16 Jun 2020 09:48:18: 26000000 INFO @ Tue, 16 Jun 2020 09:48:20: 36000000 INFO @ Tue, 16 Jun 2020 09:48:21: 22000000 INFO @ Tue, 16 Jun 2020 09:48:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:48:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:48:24: #1 total tags in treatment: 16258466 INFO @ Tue, 16 Jun 2020 09:48:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:48:24: #1 tags after filtering in treatment: 14818798 INFO @ Tue, 16 Jun 2020 09:48:24: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:48:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:25: 27000000 INFO @ Tue, 16 Jun 2020 09:48:25: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 09:48:25: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:25: #2 predicted fragment length is 126 bps INFO @ Tue, 16 Jun 2020 09:48:25: #2 alternative fragment length(s) may be 4,126,146 bps INFO @ Tue, 16 Jun 2020 09:48:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.05_model.r INFO @ Tue, 16 Jun 2020 09:48:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:27: 23000000 INFO @ Tue, 16 Jun 2020 09:48:32: 28000000 INFO @ Tue, 16 Jun 2020 09:48:34: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:39: 29000000 INFO @ Tue, 16 Jun 2020 09:48:41: 25000000 INFO @ Tue, 16 Jun 2020 09:48:46: 30000000 INFO @ Tue, 16 Jun 2020 09:48:47: 26000000 INFO @ Tue, 16 Jun 2020 09:48:52: 31000000 INFO @ Tue, 16 Jun 2020 09:48:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:54: 27000000 INFO @ Tue, 16 Jun 2020 09:48:59: 32000000 INFO @ Tue, 16 Jun 2020 09:49:01: 28000000 INFO @ Tue, 16 Jun 2020 09:49:06: 33000000 INFO @ Tue, 16 Jun 2020 09:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (469 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:07: 29000000 INFO @ Tue, 16 Jun 2020 09:49:12: 34000000 INFO @ Tue, 16 Jun 2020 09:49:14: 30000000 INFO @ Tue, 16 Jun 2020 09:49:19: 35000000 INFO @ Tue, 16 Jun 2020 09:49:21: 31000000 INFO @ Tue, 16 Jun 2020 09:49:26: 36000000 INFO @ Tue, 16 Jun 2020 09:49:28: 32000000 INFO @ Tue, 16 Jun 2020 09:49:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:30: #1 total tags in treatment: 16258466 INFO @ Tue, 16 Jun 2020 09:49:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:49:30: #1 tags after filtering in treatment: 14818798 INFO @ Tue, 16 Jun 2020 09:49:30: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:49:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:31: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 09:49:31: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:31: #2 predicted fragment length is 126 bps INFO @ Tue, 16 Jun 2020 09:49:31: #2 alternative fragment length(s) may be 4,126,146 bps INFO @ Tue, 16 Jun 2020 09:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.10_model.r INFO @ Tue, 16 Jun 2020 09:49:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:34: 33000000 INFO @ Tue, 16 Jun 2020 09:49:41: 34000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:49:47: 35000000 INFO @ Tue, 16 Jun 2020 09:49:53: 36000000 INFO @ Tue, 16 Jun 2020 09:49:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:57: #1 total tags in treatment: 16258466 INFO @ Tue, 16 Jun 2020 09:49:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:49:58: #1 tags after filtering in treatment: 14818798 INFO @ Tue, 16 Jun 2020 09:49:58: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:49:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:59: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 09:49:59: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:59: #2 predicted fragment length is 126 bps INFO @ Tue, 16 Jun 2020 09:49:59: #2 alternative fragment length(s) may be 4,126,146 bps INFO @ Tue, 16 Jun 2020 09:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.20_model.r INFO @ Tue, 16 Jun 2020 09:49:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.10_summits.bed INFO @ Tue, 16 Jun 2020 09:50:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996818/SRX4996818.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (211 records, 4 fields): 1 millis CompletedMACS2peakCalling