Job ID = 6367860 SRX = SRX4085427 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:34:20 prefetch.2.10.7: 1) Downloading 'SRR7167456'... 2020-06-15T23:34:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:21 prefetch.2.10.7: 1) 'SRR7167456' was downloaded successfully Read 31721561 spots for SRR7167456/SRR7167456.sra Written 31721561 spots for SRR7167456/SRR7167456.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: 00:23:37 31721561 reads; of these: 31721561 (100.00%) were paired; of these: 2560408 (8.07%) aligned concordantly 0 times 25226960 (79.53%) aligned concordantly exactly 1 time 3934193 (12.40%) aligned concordantly >1 times ---- 2560408 pairs aligned concordantly 0 times; of these: 141277 (5.52%) aligned discordantly 1 time ---- 2419131 pairs aligned 0 times concordantly or discordantly; of these: 4838262 mates make up the pairs; of these: 4158454 (85.95%) aligned 0 times 527719 (10.91%) aligned exactly 1 time 152089 (3.14%) aligned >1 times 93.45% overall alignment rate Time searching: 00:23:37 Overall time: 00:23:37 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 28 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] 12926830 / 29256627 = 0.4418 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 09:28:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.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 09:28:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:50: 1000000 INFO @ Tue, 16 Jun 2020 09:28:55: 2000000 INFO @ Tue, 16 Jun 2020 09:28:59: 3000000 INFO @ Tue, 16 Jun 2020 09:29:04: 4000000 INFO @ Tue, 16 Jun 2020 09:29:09: 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 09:29:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.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 09:29:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:14: 6000000 INFO @ Tue, 16 Jun 2020 09:29:19: 1000000 INFO @ Tue, 16 Jun 2020 09:29:19: 7000000 INFO @ Tue, 16 Jun 2020 09:29:24: 8000000 INFO @ Tue, 16 Jun 2020 09:29:24: 2000000 INFO @ Tue, 16 Jun 2020 09:29:29: 9000000 INFO @ Tue, 16 Jun 2020 09:29:31: 3000000 INFO @ Tue, 16 Jun 2020 09:29:35: 10000000 INFO @ Tue, 16 Jun 2020 09:29:37: 4000000 INFO @ Tue, 16 Jun 2020 09:29:40: 11000000 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 09:29:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.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 09:29:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:43: 5000000 INFO @ Tue, 16 Jun 2020 09:29:46: 12000000 INFO @ Tue, 16 Jun 2020 09:29:48: 1000000 INFO @ Tue, 16 Jun 2020 09:29:49: 6000000 INFO @ Tue, 16 Jun 2020 09:29:51: 13000000 INFO @ Tue, 16 Jun 2020 09:29:54: 2000000 INFO @ Tue, 16 Jun 2020 09:29:55: 7000000 INFO @ Tue, 16 Jun 2020 09:29:56: 14000000 INFO @ Tue, 16 Jun 2020 09:29:59: 3000000 INFO @ Tue, 16 Jun 2020 09:30:01: 8000000 INFO @ Tue, 16 Jun 2020 09:30:02: 15000000 INFO @ Tue, 16 Jun 2020 09:30:04: 4000000 INFO @ Tue, 16 Jun 2020 09:30:07: 9000000 INFO @ Tue, 16 Jun 2020 09:30:07: 16000000 INFO @ Tue, 16 Jun 2020 09:30:10: 5000000 INFO @ Tue, 16 Jun 2020 09:30:13: 17000000 INFO @ Tue, 16 Jun 2020 09:30:13: 10000000 INFO @ Tue, 16 Jun 2020 09:30:15: 6000000 INFO @ Tue, 16 Jun 2020 09:30:18: 18000000 INFO @ Tue, 16 Jun 2020 09:30:19: 11000000 INFO @ Tue, 16 Jun 2020 09:30:21: 7000000 INFO @ Tue, 16 Jun 2020 09:30:23: 19000000 INFO @ Tue, 16 Jun 2020 09:30:25: 12000000 INFO @ Tue, 16 Jun 2020 09:30:26: 8000000 INFO @ Tue, 16 Jun 2020 09:30:29: 20000000 INFO @ Tue, 16 Jun 2020 09:30:31: 13000000 INFO @ Tue, 16 Jun 2020 09:30:31: 9000000 INFO @ Tue, 16 Jun 2020 09:30:34: 21000000 INFO @ Tue, 16 Jun 2020 09:30:37: 10000000 INFO @ Tue, 16 Jun 2020 09:30:37: 14000000 INFO @ Tue, 16 Jun 2020 09:30:39: 22000000 INFO @ Tue, 16 Jun 2020 09:30:42: 11000000 INFO @ Tue, 16 Jun 2020 09:30:43: 15000000 INFO @ Tue, 16 Jun 2020 09:30:44: 23000000 INFO @ Tue, 16 Jun 2020 09:30:48: 12000000 INFO @ Tue, 16 Jun 2020 09:30:49: 16000000 INFO @ Tue, 16 Jun 2020 09:30:50: 24000000 INFO @ Tue, 16 Jun 2020 09:30:53: 13000000 INFO @ Tue, 16 Jun 2020 09:30:55: 17000000 INFO @ Tue, 16 Jun 2020 09:30:55: 25000000 INFO @ Tue, 16 Jun 2020 09:30:58: 14000000 INFO @ Tue, 16 Jun 2020 09:31:00: 26000000 INFO @ Tue, 16 Jun 2020 09:31:01: 18000000 INFO @ Tue, 16 Jun 2020 09:31:04: 15000000 INFO @ Tue, 16 Jun 2020 09:31:05: 27000000 INFO @ Tue, 16 Jun 2020 09:31:07: 19000000 INFO @ Tue, 16 Jun 2020 09:31:09: 16000000 INFO @ Tue, 16 Jun 2020 09:31:11: 28000000 INFO @ Tue, 16 Jun 2020 09:31:13: 20000000 INFO @ Tue, 16 Jun 2020 09:31:14: 17000000 INFO @ Tue, 16 Jun 2020 09:31:16: 29000000 INFO @ Tue, 16 Jun 2020 09:31:19: 21000000 INFO @ Tue, 16 Jun 2020 09:31:20: 18000000 INFO @ Tue, 16 Jun 2020 09:31:21: 30000000 INFO @ Tue, 16 Jun 2020 09:31:24: 22000000 INFO @ Tue, 16 Jun 2020 09:31:25: 19000000 INFO @ Tue, 16 Jun 2020 09:31:26: 31000000 INFO @ Tue, 16 Jun 2020 09:31:30: 23000000 INFO @ Tue, 16 Jun 2020 09:31:30: 20000000 INFO @ Tue, 16 Jun 2020 09:31:32: 32000000 INFO @ Tue, 16 Jun 2020 09:31:36: 21000000 INFO @ Tue, 16 Jun 2020 09:31:36: 24000000 INFO @ Tue, 16 Jun 2020 09:31:37: 33000000 INFO @ Tue, 16 Jun 2020 09:31:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:39: #1 total tags in treatment: 16274814 INFO @ Tue, 16 Jun 2020 09:31:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:39: #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 09:31:39: #1 tags after filtering in treatment: 12949350 INFO @ Tue, 16 Jun 2020 09:31:39: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 09:31:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:40: #2 number of paired peaks: 245 WARNING @ Tue, 16 Jun 2020 09:31:40: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:40: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 09:31:40: #2 alternative fragment length(s) may be 3,124 bps INFO @ Tue, 16 Jun 2020 09:31:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.05_model.r INFO @ Tue, 16 Jun 2020 09:31:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:41: 22000000 INFO @ Tue, 16 Jun 2020 09:31:42: 25000000 INFO @ Tue, 16 Jun 2020 09:31:46: 23000000 INFO @ Tue, 16 Jun 2020 09:31:48: 26000000 INFO @ Tue, 16 Jun 2020 09:31:52: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:31:54: 27000000 INFO @ Tue, 16 Jun 2020 09:31:57: 25000000 INFO @ Tue, 16 Jun 2020 09:32:00: 28000000 INFO @ Tue, 16 Jun 2020 09:32:02: 26000000 INFO @ Tue, 16 Jun 2020 09:32:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:05: 29000000 INFO @ Tue, 16 Jun 2020 09:32:08: 27000000 INFO @ Tue, 16 Jun 2020 09:32:11: 30000000 INFO @ Tue, 16 Jun 2020 09:32:13: 28000000 INFO @ Tue, 16 Jun 2020 09:32:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:16: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1359 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:17: 31000000 INFO @ Tue, 16 Jun 2020 09:32:18: 29000000 INFO @ Tue, 16 Jun 2020 09:32:23: 32000000 INFO @ Tue, 16 Jun 2020 09:32:23: 30000000 INFO @ Tue, 16 Jun 2020 09:32:29: 33000000 INFO @ Tue, 16 Jun 2020 09:32:29: 31000000 INFO @ Tue, 16 Jun 2020 09:32:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:31: #1 total tags in treatment: 16274814 INFO @ Tue, 16 Jun 2020 09:32:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:31: #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 09:32:31: #1 tags after filtering in treatment: 12949350 INFO @ Tue, 16 Jun 2020 09:32:31: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 09:32:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:32: #2 number of paired peaks: 245 WARNING @ Tue, 16 Jun 2020 09:32:32: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:32: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 09:32:32: #2 alternative fragment length(s) may be 3,124 bps INFO @ Tue, 16 Jun 2020 09:32:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.10_model.r INFO @ Tue, 16 Jun 2020 09:32:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:34: 32000000 INFO @ Tue, 16 Jun 2020 09:32:39: 33000000 INFO @ Tue, 16 Jun 2020 09:32:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:41: #1 total tags in treatment: 16274814 INFO @ Tue, 16 Jun 2020 09:32:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:41: #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 09:32:41: #1 tags after filtering in treatment: 12949350 INFO @ Tue, 16 Jun 2020 09:32:41: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 09:32:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:42: #2 number of paired peaks: 245 WARNING @ Tue, 16 Jun 2020 09:32:42: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:42: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 09:32:42: #2 alternative fragment length(s) may be 3,124 bps INFO @ Tue, 16 Jun 2020 09:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.20_model.r INFO @ Tue, 16 Jun 2020 09:32:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (666 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085427/SRX4085427.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 1 millis CompletedMACS2peakCalling