Job ID = 6368917 SRX = SRX7175089 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:34:50 prefetch.2.10.7: 1) Downloading 'SRR10485521'... 2020-06-16T00:34:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:17 prefetch.2.10.7: 1) 'SRR10485521' was downloaded successfully 2020-06-16T00:39:17 prefetch.2.10.7: 'SRR10485521' has 0 unresolved dependencies Read 27099673 spots for SRR10485521/SRR10485521.sra Written 27099673 spots for SRR10485521/SRR10485521.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: 00:00:01 Multiseed full-index search: 00:12:57 27099673 reads; of these: 27099673 (100.00%) were paired; of these: 14840256 (54.76%) aligned concordantly 0 times 10627344 (39.22%) aligned concordantly exactly 1 time 1632073 (6.02%) aligned concordantly >1 times ---- 14840256 pairs aligned concordantly 0 times; of these: 825197 (5.56%) aligned discordantly 1 time ---- 14015059 pairs aligned 0 times concordantly or discordantly; of these: 28030118 mates make up the pairs; of these: 26986075 (96.28%) aligned 0 times 693794 (2.48%) aligned exactly 1 time 350249 (1.25%) aligned >1 times 50.21% overall alignment rate Time searching: 00:12:58 Overall time: 00:12:58 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] 2278315 / 13070551 = 0.1743 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 10:01:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.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 10:01:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:01:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:01:48: 1000000 INFO @ Tue, 16 Jun 2020 10:01:54: 2000000 INFO @ Tue, 16 Jun 2020 10:01:59: 3000000 INFO @ Tue, 16 Jun 2020 10:02:04: 4000000 INFO @ Tue, 16 Jun 2020 10:02:09: 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 10:02:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.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 10:02:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:14: 6000000 INFO @ Tue, 16 Jun 2020 10:02:19: 1000000 INFO @ Tue, 16 Jun 2020 10:02:19: 7000000 INFO @ Tue, 16 Jun 2020 10:02:24: 2000000 INFO @ Tue, 16 Jun 2020 10:02:25: 8000000 INFO @ Tue, 16 Jun 2020 10:02:30: 3000000 INFO @ Tue, 16 Jun 2020 10:02:30: 9000000 INFO @ Tue, 16 Jun 2020 10:02:36: 4000000 INFO @ Tue, 16 Jun 2020 10:02:36: 10000000 INFO @ Tue, 16 Jun 2020 10:02:41: 5000000 INFO @ Tue, 16 Jun 2020 10:02:41: 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 10:02:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.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 10:02:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:47: 12000000 INFO @ Tue, 16 Jun 2020 10:02:47: 6000000 INFO @ Tue, 16 Jun 2020 10:02:49: 1000000 INFO @ Tue, 16 Jun 2020 10:02:52: 7000000 INFO @ Tue, 16 Jun 2020 10:02:52: 13000000 INFO @ Tue, 16 Jun 2020 10:02:54: 2000000 INFO @ Tue, 16 Jun 2020 10:02:58: 8000000 INFO @ Tue, 16 Jun 2020 10:02:58: 14000000 INFO @ Tue, 16 Jun 2020 10:03:00: 3000000 INFO @ Tue, 16 Jun 2020 10:03:03: 9000000 INFO @ Tue, 16 Jun 2020 10:03:04: 15000000 INFO @ Tue, 16 Jun 2020 10:03:06: 4000000 INFO @ Tue, 16 Jun 2020 10:03:09: 10000000 INFO @ Tue, 16 Jun 2020 10:03:09: 16000000 INFO @ Tue, 16 Jun 2020 10:03:11: 5000000 INFO @ Tue, 16 Jun 2020 10:03:15: 11000000 INFO @ Tue, 16 Jun 2020 10:03:15: 17000000 INFO @ Tue, 16 Jun 2020 10:03:17: 6000000 INFO @ Tue, 16 Jun 2020 10:03:20: 12000000 INFO @ Tue, 16 Jun 2020 10:03:21: 18000000 INFO @ Tue, 16 Jun 2020 10:03:22: 7000000 INFO @ Tue, 16 Jun 2020 10:03:26: 13000000 INFO @ Tue, 16 Jun 2020 10:03:26: 19000000 INFO @ Tue, 16 Jun 2020 10:03:28: 8000000 INFO @ Tue, 16 Jun 2020 10:03:31: 14000000 INFO @ Tue, 16 Jun 2020 10:03:32: 20000000 INFO @ Tue, 16 Jun 2020 10:03:33: 9000000 INFO @ Tue, 16 Jun 2020 10:03:37: 15000000 INFO @ Tue, 16 Jun 2020 10:03:37: 21000000 INFO @ Tue, 16 Jun 2020 10:03:39: 10000000 INFO @ Tue, 16 Jun 2020 10:03:43: 16000000 INFO @ Tue, 16 Jun 2020 10:03:43: 22000000 INFO @ Tue, 16 Jun 2020 10:03:44: 11000000 INFO @ Tue, 16 Jun 2020 10:03:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:03:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:03:47: #1 total tags in treatment: 10076226 INFO @ Tue, 16 Jun 2020 10:03:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:03:47: #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 10:03:47: #1 tags after filtering in treatment: 9342542 INFO @ Tue, 16 Jun 2020 10:03:47: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 10:03:47: #1 finished! INFO @ Tue, 16 Jun 2020 10:03:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:03:48: #2 number of paired peaks: 405 WARNING @ Tue, 16 Jun 2020 10:03:48: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Tue, 16 Jun 2020 10:03:48: start model_add_line... INFO @ Tue, 16 Jun 2020 10:03:48: start X-correlation... INFO @ Tue, 16 Jun 2020 10:03:48: end of X-cor INFO @ Tue, 16 Jun 2020 10:03:48: #2 finished! INFO @ Tue, 16 Jun 2020 10:03:48: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 10:03:48: #2 alternative fragment length(s) may be 4,146 bps INFO @ Tue, 16 Jun 2020 10:03:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.05_model.r INFO @ Tue, 16 Jun 2020 10:03:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:03:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:03:48: 17000000 INFO @ Tue, 16 Jun 2020 10:03:50: 12000000 INFO @ Tue, 16 Jun 2020 10:03:54: 18000000 INFO @ Tue, 16 Jun 2020 10:03:55: 13000000 INFO @ Tue, 16 Jun 2020 10:03:59: 19000000 INFO @ Tue, 16 Jun 2020 10:04:01: 14000000 INFO @ Tue, 16 Jun 2020 10:04:05: 20000000 INFO @ Tue, 16 Jun 2020 10:04:06: 15000000 INFO @ Tue, 16 Jun 2020 10:04:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:04:10: 21000000 INFO @ Tue, 16 Jun 2020 10:04:12: 16000000 INFO @ Tue, 16 Jun 2020 10:04:16: 22000000 INFO @ Tue, 16 Jun 2020 10:04:17: 17000000 INFO @ Tue, 16 Jun 2020 10:04:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:04:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:04:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.05_summits.bed INFO @ Tue, 16 Jun 2020 10:04:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:04:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:04:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:04:19: #1 total tags in treatment: 10076226 INFO @ Tue, 16 Jun 2020 10:04:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:04:19: #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 10:04:20: #1 tags after filtering in treatment: 9342542 INFO @ Tue, 16 Jun 2020 10:04:20: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 10:04:20: #1 finished! INFO @ Tue, 16 Jun 2020 10:04:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:04:20: #2 number of paired peaks: 405 WARNING @ Tue, 16 Jun 2020 10:04:20: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Tue, 16 Jun 2020 10:04:20: start model_add_line... INFO @ Tue, 16 Jun 2020 10:04:20: start X-correlation... INFO @ Tue, 16 Jun 2020 10:04:20: end of X-cor INFO @ Tue, 16 Jun 2020 10:04:20: #2 finished! INFO @ Tue, 16 Jun 2020 10:04:20: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 10:04:20: #2 alternative fragment length(s) may be 4,146 bps INFO @ Tue, 16 Jun 2020 10:04:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.10_model.r INFO @ Tue, 16 Jun 2020 10:04:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:04:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:04:22: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:04:28: 19000000 INFO @ Tue, 16 Jun 2020 10:04:33: 20000000 INFO @ Tue, 16 Jun 2020 10:04:38: 21000000 INFO @ Tue, 16 Jun 2020 10:04:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:04:43: 22000000 INFO @ Tue, 16 Jun 2020 10:04:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:04:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:04:46: #1 total tags in treatment: 10076226 INFO @ Tue, 16 Jun 2020 10:04:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:04:46: #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 10:04:47: #1 tags after filtering in treatment: 9342542 INFO @ Tue, 16 Jun 2020 10:04:47: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 10:04:47: #1 finished! INFO @ Tue, 16 Jun 2020 10:04:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:04:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:04:47: #2 number of paired peaks: 405 WARNING @ Tue, 16 Jun 2020 10:04:47: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Tue, 16 Jun 2020 10:04:47: start model_add_line... INFO @ Tue, 16 Jun 2020 10:04:47: start X-correlation... INFO @ Tue, 16 Jun 2020 10:04:47: end of X-cor INFO @ Tue, 16 Jun 2020 10:04:47: #2 finished! INFO @ Tue, 16 Jun 2020 10:04:47: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 10:04:47: #2 alternative fragment length(s) may be 4,146 bps INFO @ Tue, 16 Jun 2020 10:04:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.20_model.r INFO @ Tue, 16 Jun 2020 10:04:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:04:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:04:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.10_summits.bed INFO @ Tue, 16 Jun 2020 10:04:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (268 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:05:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:05:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:05:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7175089/SRX7175089.20_summits.bed INFO @ Tue, 16 Jun 2020 10:05:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (191 records, 4 fields): 1 millis CompletedMACS2peakCalling