Job ID = 6367953 SRX = SRX4419819 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:46:02 prefetch.2.10.7: 1) Downloading 'SRR7553944'... 2020-06-15T23:46:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:29 prefetch.2.10.7: 'SRR7553944' is valid 2020-06-15T23:48:29 prefetch.2.10.7: 1) 'SRR7553944' was downloaded successfully Read 10723173 spots for SRR7553944/SRR7553944.sra Written 10723173 spots for SRR7553944/SRR7553944.sra 2020-06-15T23:49:35 prefetch.2.10.7: 1) Downloading 'SRR7553945'... 2020-06-15T23:49:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:30 prefetch.2.10.7: 'SRR7553945' is valid 2020-06-15T23:50:30 prefetch.2.10.7: 1) 'SRR7553945' was downloaded successfully Read 3562823 spots for SRR7553945/SRR7553945.sra Written 3562823 spots for SRR7553945/SRR7553945.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: 00:11:37 14285996 reads; of these: 14285996 (100.00%) were paired; of these: 1487946 (10.42%) aligned concordantly 0 times 10880101 (76.16%) aligned concordantly exactly 1 time 1917949 (13.43%) aligned concordantly >1 times ---- 1487946 pairs aligned concordantly 0 times; of these: 323523 (21.74%) aligned discordantly 1 time ---- 1164423 pairs aligned 0 times concordantly or discordantly; of these: 2328846 mates make up the pairs; of these: 1818203 (78.07%) aligned 0 times 338276 (14.53%) aligned exactly 1 time 172367 (7.40%) aligned >1 times 93.64% overall alignment rate Time searching: 00:11:37 Overall time: 00:11:37 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 12 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] 435454 / 13027996 = 0.0334 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 09:08:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.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 09:08:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:48: 1000000 INFO @ Tue, 16 Jun 2020 09:08:53: 2000000 INFO @ Tue, 16 Jun 2020 09:08:58: 3000000 INFO @ Tue, 16 Jun 2020 09:09:03: 4000000 INFO @ Tue, 16 Jun 2020 09:09:07: 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 09:09:12: 6000000 INFO @ Tue, 16 Jun 2020 09:09:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.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 09:09:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:17: 7000000 INFO @ Tue, 16 Jun 2020 09:09:18: 1000000 INFO @ Tue, 16 Jun 2020 09:09:22: 8000000 INFO @ Tue, 16 Jun 2020 09:09:23: 2000000 INFO @ Tue, 16 Jun 2020 09:09:27: 9000000 INFO @ Tue, 16 Jun 2020 09:09:28: 3000000 INFO @ Tue, 16 Jun 2020 09:09:32: 10000000 INFO @ Tue, 16 Jun 2020 09:09:33: 4000000 INFO @ Tue, 16 Jun 2020 09:09:37: 11000000 INFO @ Tue, 16 Jun 2020 09:09:38: 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 09:09:42: 12000000 INFO @ Tue, 16 Jun 2020 09:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.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 09:09:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:44: 6000000 INFO @ Tue, 16 Jun 2020 09:09:47: 13000000 INFO @ Tue, 16 Jun 2020 09:09:47: 1000000 INFO @ Tue, 16 Jun 2020 09:09:49: 7000000 INFO @ Tue, 16 Jun 2020 09:09:52: 2000000 INFO @ Tue, 16 Jun 2020 09:09:52: 14000000 INFO @ Tue, 16 Jun 2020 09:09:54: 8000000 INFO @ Tue, 16 Jun 2020 09:09:56: 3000000 INFO @ Tue, 16 Jun 2020 09:09:57: 15000000 INFO @ Tue, 16 Jun 2020 09:09:59: 9000000 INFO @ Tue, 16 Jun 2020 09:10:00: 4000000 INFO @ Tue, 16 Jun 2020 09:10:02: 16000000 INFO @ Tue, 16 Jun 2020 09:10:04: 10000000 INFO @ Tue, 16 Jun 2020 09:10:05: 5000000 INFO @ Tue, 16 Jun 2020 09:10:08: 17000000 INFO @ Tue, 16 Jun 2020 09:10:09: 11000000 INFO @ Tue, 16 Jun 2020 09:10:09: 6000000 INFO @ Tue, 16 Jun 2020 09:10:13: 18000000 INFO @ Tue, 16 Jun 2020 09:10:13: 7000000 INFO @ Tue, 16 Jun 2020 09:10:14: 12000000 INFO @ Tue, 16 Jun 2020 09:10:18: 19000000 INFO @ Tue, 16 Jun 2020 09:10:18: 8000000 INFO @ Tue, 16 Jun 2020 09:10:19: 13000000 INFO @ Tue, 16 Jun 2020 09:10:22: 9000000 INFO @ Tue, 16 Jun 2020 09:10:23: 20000000 INFO @ Tue, 16 Jun 2020 09:10:24: 14000000 INFO @ Tue, 16 Jun 2020 09:10:27: 10000000 INFO @ Tue, 16 Jun 2020 09:10:28: 21000000 INFO @ Tue, 16 Jun 2020 09:10:29: 15000000 INFO @ Tue, 16 Jun 2020 09:10:31: 11000000 INFO @ Tue, 16 Jun 2020 09:10:33: 22000000 INFO @ Tue, 16 Jun 2020 09:10:34: 16000000 INFO @ Tue, 16 Jun 2020 09:10:35: 12000000 INFO @ Tue, 16 Jun 2020 09:10:38: 23000000 INFO @ Tue, 16 Jun 2020 09:10:39: 17000000 INFO @ Tue, 16 Jun 2020 09:10:40: 13000000 INFO @ Tue, 16 Jun 2020 09:10:43: 24000000 INFO @ Tue, 16 Jun 2020 09:10:44: 18000000 INFO @ Tue, 16 Jun 2020 09:10:44: 14000000 INFO @ Tue, 16 Jun 2020 09:10:48: 25000000 INFO @ Tue, 16 Jun 2020 09:10:48: 15000000 INFO @ Tue, 16 Jun 2020 09:10:49: 19000000 INFO @ Tue, 16 Jun 2020 09:10:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:10:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:10:53: #1 total tags in treatment: 12365824 INFO @ Tue, 16 Jun 2020 09:10:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:53: #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 09:10:53: 16000000 INFO @ Tue, 16 Jun 2020 09:10:53: #1 tags after filtering in treatment: 10735844 INFO @ Tue, 16 Jun 2020 09:10:53: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:10:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:54: #2 number of paired peaks: 216 WARNING @ Tue, 16 Jun 2020 09:10:54: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:54: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 09:10:54: #2 alternative fragment length(s) may be 4,68,144,162 bps INFO @ Tue, 16 Jun 2020 09:10:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.05_model.r INFO @ Tue, 16 Jun 2020 09:10:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:54: 20000000 INFO @ Tue, 16 Jun 2020 09:10:57: 17000000 INFO @ Tue, 16 Jun 2020 09:10:59: 21000000 INFO @ Tue, 16 Jun 2020 09:11:01: 18000000 INFO @ Tue, 16 Jun 2020 09:11:04: 22000000 INFO @ Tue, 16 Jun 2020 09:11:06: 19000000 INFO @ Tue, 16 Jun 2020 09:11:09: 23000000 INFO @ Tue, 16 Jun 2020 09:11:10: 20000000 INFO @ Tue, 16 Jun 2020 09:11:14: 24000000 INFO @ Tue, 16 Jun 2020 09:11:14: 21000000 INFO @ Tue, 16 Jun 2020 09:11:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:19: 22000000 INFO @ Tue, 16 Jun 2020 09:11:19: 25000000 INFO @ Tue, 16 Jun 2020 09:11:23: 23000000 INFO @ Tue, 16 Jun 2020 09:11:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:23: #1 total tags in treatment: 12365824 INFO @ Tue, 16 Jun 2020 09:11:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:23: #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 09:11:24: #1 tags after filtering in treatment: 10735844 INFO @ Tue, 16 Jun 2020 09:11:24: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:11:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:24: #2 number of paired peaks: 216 WARNING @ Tue, 16 Jun 2020 09:11:24: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:24: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 09:11:24: #2 alternative fragment length(s) may be 4,68,144,162 bps INFO @ Tue, 16 Jun 2020 09:11:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.10_model.r INFO @ Tue, 16 Jun 2020 09:11:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (262 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:27: 24000000 INFO @ Tue, 16 Jun 2020 09:11:31: 25000000 INFO @ Tue, 16 Jun 2020 09:11:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:35: #1 total tags in treatment: 12365824 INFO @ Tue, 16 Jun 2020 09:11:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:35: #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 09:11:35: #1 tags after filtering in treatment: 10735844 INFO @ Tue, 16 Jun 2020 09:11:35: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:11:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:36: #2 number of paired peaks: 216 WARNING @ Tue, 16 Jun 2020 09:11:36: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:36: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 09:11:36: #2 alternative fragment length(s) may be 4,68,144,162 bps INFO @ Tue, 16 Jun 2020 09:11:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.20_model.r INFO @ Tue, 16 Jun 2020 09:11:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.10_summits.bed INFO @ Tue, 16 Jun 2020 09:11:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (194 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4419819/SRX4419819.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (127 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。