Job ID = 6368450 SRX = SRX4996806 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 'SRR8176692'... 2020-06-16T00:13:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:23 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:23 prefetch.2.10.7: 1) 'SRR8176692' was downloaded successfully 2020-06-16T00:16:23 prefetch.2.10.7: 'SRR8176692' has 0 unresolved dependencies Read 18937560 spots for SRR8176692/SRR8176692.sra Written 18937560 spots for SRR8176692/SRR8176692.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: 00:20:18 18937560 reads; of these: 18937560 (100.00%) were paired; of these: 2052115 (10.84%) aligned concordantly 0 times 14266403 (75.33%) aligned concordantly exactly 1 time 2619042 (13.83%) aligned concordantly >1 times ---- 2052115 pairs aligned concordantly 0 times; of these: 646623 (31.51%) aligned discordantly 1 time ---- 1405492 pairs aligned 0 times concordantly or discordantly; of these: 2810984 mates make up the pairs; of these: 2324178 (82.68%) aligned 0 times 285982 (10.17%) aligned exactly 1 time 200824 (7.14%) aligned >1 times 93.86% overall alignment rate Time searching: 00:20:18 Overall time: 00:20:18 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] 2030217 / 17522793 = 0.1159 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 09:49:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.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 09:49:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:07: 1000000 INFO @ Tue, 16 Jun 2020 09:49:12: 2000000 INFO @ Tue, 16 Jun 2020 09:49:17: 3000000 INFO @ Tue, 16 Jun 2020 09:49:22: 4000000 INFO @ Tue, 16 Jun 2020 09:49:26: 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 09:49:31: 6000000 INFO @ Tue, 16 Jun 2020 09:49:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.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 09:49:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:36: 7000000 INFO @ Tue, 16 Jun 2020 09:49:37: 1000000 INFO @ Tue, 16 Jun 2020 09:49:42: 8000000 INFO @ Tue, 16 Jun 2020 09:49:42: 2000000 INFO @ Tue, 16 Jun 2020 09:49:47: 9000000 INFO @ Tue, 16 Jun 2020 09:49:47: 3000000 INFO @ Tue, 16 Jun 2020 09:49:52: 10000000 INFO @ Tue, 16 Jun 2020 09:49:52: 4000000 INFO @ Tue, 16 Jun 2020 09:49:57: 11000000 INFO @ Tue, 16 Jun 2020 09:49:57: 5000000 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 09:50:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.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 09:50:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:03: 12000000 INFO @ Tue, 16 Jun 2020 09:50:03: 6000000 INFO @ Tue, 16 Jun 2020 09:50:07: 1000000 INFO @ Tue, 16 Jun 2020 09:50:09: 13000000 INFO @ Tue, 16 Jun 2020 09:50:09: 7000000 INFO @ Tue, 16 Jun 2020 09:50:13: 2000000 INFO @ Tue, 16 Jun 2020 09:50:14: 14000000 INFO @ Tue, 16 Jun 2020 09:50:15: 8000000 INFO @ Tue, 16 Jun 2020 09:50:19: 3000000 INFO @ Tue, 16 Jun 2020 09:50:20: 15000000 INFO @ Tue, 16 Jun 2020 09:50:21: 9000000 INFO @ Tue, 16 Jun 2020 09:50:25: 4000000 INFO @ Tue, 16 Jun 2020 09:50:26: 16000000 INFO @ Tue, 16 Jun 2020 09:50:27: 10000000 INFO @ Tue, 16 Jun 2020 09:50:32: 5000000 INFO @ Tue, 16 Jun 2020 09:50:32: 17000000 INFO @ Tue, 16 Jun 2020 09:50:33: 11000000 INFO @ Tue, 16 Jun 2020 09:50:38: 6000000 INFO @ Tue, 16 Jun 2020 09:50:38: 18000000 INFO @ Tue, 16 Jun 2020 09:50:39: 12000000 INFO @ Tue, 16 Jun 2020 09:50:44: 7000000 INFO @ Tue, 16 Jun 2020 09:50:44: 19000000 INFO @ Tue, 16 Jun 2020 09:50:45: 13000000 INFO @ Tue, 16 Jun 2020 09:50:50: 8000000 INFO @ Tue, 16 Jun 2020 09:50:50: 20000000 INFO @ Tue, 16 Jun 2020 09:50:51: 14000000 INFO @ Tue, 16 Jun 2020 09:50:56: 9000000 INFO @ Tue, 16 Jun 2020 09:50:56: 21000000 INFO @ Tue, 16 Jun 2020 09:50:57: 15000000 INFO @ Tue, 16 Jun 2020 09:51:02: 10000000 INFO @ Tue, 16 Jun 2020 09:51:02: 22000000 INFO @ Tue, 16 Jun 2020 09:51:03: 16000000 INFO @ Tue, 16 Jun 2020 09:51:08: 23000000 INFO @ Tue, 16 Jun 2020 09:51:08: 11000000 INFO @ Tue, 16 Jun 2020 09:51:09: 17000000 INFO @ Tue, 16 Jun 2020 09:51:14: 24000000 INFO @ Tue, 16 Jun 2020 09:51:14: 12000000 INFO @ Tue, 16 Jun 2020 09:51:15: 18000000 INFO @ Tue, 16 Jun 2020 09:51:19: 25000000 INFO @ Tue, 16 Jun 2020 09:51:20: 13000000 INFO @ Tue, 16 Jun 2020 09:51:20: 19000000 INFO @ Tue, 16 Jun 2020 09:51:25: 26000000 INFO @ Tue, 16 Jun 2020 09:51:26: 14000000 INFO @ Tue, 16 Jun 2020 09:51:26: 20000000 INFO @ Tue, 16 Jun 2020 09:51:31: 27000000 INFO @ Tue, 16 Jun 2020 09:51:32: 15000000 INFO @ Tue, 16 Jun 2020 09:51:32: 21000000 INFO @ Tue, 16 Jun 2020 09:51:37: 28000000 INFO @ Tue, 16 Jun 2020 09:51:38: 16000000 INFO @ Tue, 16 Jun 2020 09:51:38: 22000000 INFO @ Tue, 16 Jun 2020 09:51:43: 29000000 INFO @ Tue, 16 Jun 2020 09:51:44: 23000000 INFO @ Tue, 16 Jun 2020 09:51:44: 17000000 INFO @ Tue, 16 Jun 2020 09:51:49: 30000000 INFO @ Tue, 16 Jun 2020 09:51:50: 24000000 INFO @ Tue, 16 Jun 2020 09:51:50: 18000000 INFO @ Tue, 16 Jun 2020 09:51:55: 31000000 INFO @ Tue, 16 Jun 2020 09:51:56: 25000000 INFO @ Tue, 16 Jun 2020 09:51:56: 19000000 INFO @ Tue, 16 Jun 2020 09:51:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:57: #1 total tags in treatment: 14880739 INFO @ Tue, 16 Jun 2020 09:51:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:57: #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 09:51:58: #1 tags after filtering in treatment: 13620178 INFO @ Tue, 16 Jun 2020 09:51:58: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:51:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:59: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 09:51:59: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:59: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 09:51:59: #2 alternative fragment length(s) may be 4,142 bps INFO @ Tue, 16 Jun 2020 09:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.05_model.r INFO @ Tue, 16 Jun 2020 09:51:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:01: 26000000 INFO @ Tue, 16 Jun 2020 09:52:02: 20000000 INFO @ Tue, 16 Jun 2020 09:52:07: 27000000 INFO @ Tue, 16 Jun 2020 09:52:07: 21000000 INFO @ Tue, 16 Jun 2020 09:52:12: 28000000 INFO @ Tue, 16 Jun 2020 09:52:13: 22000000 INFO @ Tue, 16 Jun 2020 09:52:17: 29000000 INFO @ Tue, 16 Jun 2020 09:52:18: 23000000 INFO @ Tue, 16 Jun 2020 09:52:23: 30000000 INFO @ Tue, 16 Jun 2020 09:52:23: 24000000 INFO @ Tue, 16 Jun 2020 09:52:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:28: 31000000 INFO @ Tue, 16 Jun 2020 09:52:29: 25000000 INFO @ Tue, 16 Jun 2020 09:52:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:31: #1 total tags in treatment: 14880739 INFO @ Tue, 16 Jun 2020 09:52:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:31: #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 09:52:31: #1 tags after filtering in treatment: 13620178 INFO @ Tue, 16 Jun 2020 09:52:31: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:52:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:31: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:52:32: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 09:52:32: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:32: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 09:52:32: #2 alternative fragment length(s) may be 4,142 bps INFO @ Tue, 16 Jun 2020 09:52:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.10_model.r INFO @ Tue, 16 Jun 2020 09:52:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:34: 26000000 INFO @ Tue, 16 Jun 2020 09:52:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.05_summits.bed INFO @ Tue, 16 Jun 2020 09:52:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (462 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:39: 27000000 INFO @ Tue, 16 Jun 2020 09:52:44: 28000000 INFO @ Tue, 16 Jun 2020 09:52:49: 29000000 INFO @ Tue, 16 Jun 2020 09:52:54: 30000000 INFO @ Tue, 16 Jun 2020 09:52:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:00: 31000000 INFO @ Tue, 16 Jun 2020 09:53:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:02: #1 total tags in treatment: 14880739 INFO @ Tue, 16 Jun 2020 09:53:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:02: #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 09:53:02: #1 tags after filtering in treatment: 13620178 INFO @ Tue, 16 Jun 2020 09:53:02: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:53:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:03: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 09:53:03: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:04: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 09:53:04: #2 alternative fragment length(s) may be 4,142 bps INFO @ Tue, 16 Jun 2020 09:53:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.20_model.r INFO @ Tue, 16 Jun 2020 09:53:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996806/SRX4996806.20_summits.bed INFO @ Tue, 16 Jun 2020 09:53:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。