Job ID = 6367823 SRX = SRX4085391 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:45:44 prefetch.2.10.7: 1) Downloading 'SRR7167420'... 2020-06-15T23:45:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:59 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:59 prefetch.2.10.7: 1) 'SRR7167420' was downloaded successfully Read 11256736 spots for SRR7167420/SRR7167420.sra Written 11256736 spots for SRR7167420/SRR7167420.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: 00:06:51 11256736 reads; of these: 11256736 (100.00%) were paired; of these: 6915849 (61.44%) aligned concordantly 0 times 3693196 (32.81%) aligned concordantly exactly 1 time 647691 (5.75%) aligned concordantly >1 times ---- 6915849 pairs aligned concordantly 0 times; of these: 328137 (4.74%) aligned discordantly 1 time ---- 6587712 pairs aligned 0 times concordantly or discordantly; of these: 13175424 mates make up the pairs; of these: 9683484 (73.50%) aligned 0 times 2980461 (22.62%) aligned exactly 1 time 511479 (3.88%) aligned >1 times 56.99% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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 8 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] 319534 / 4507638 = 0.0709 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 09:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.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 09:01:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:22: 1000000 INFO @ Tue, 16 Jun 2020 09:01:27: 2000000 INFO @ Tue, 16 Jun 2020 09:01:33: 3000000 INFO @ Tue, 16 Jun 2020 09:01:38: 4000000 INFO @ Tue, 16 Jun 2020 09:01:43: 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 09:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.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 09:01:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:49: 6000000 INFO @ Tue, 16 Jun 2020 09:01:51: 1000000 INFO @ Tue, 16 Jun 2020 09:01:54: 7000000 INFO @ Tue, 16 Jun 2020 09:01:57: 2000000 INFO @ Tue, 16 Jun 2020 09:02:00: 8000000 INFO @ Tue, 16 Jun 2020 09:02:02: 3000000 INFO @ Tue, 16 Jun 2020 09:02:05: 9000000 INFO @ Tue, 16 Jun 2020 09:02:08: 4000000 INFO @ Tue, 16 Jun 2020 09:02:10: 10000000 INFO @ Tue, 16 Jun 2020 09:02:14: 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 09:02:16: 11000000 INFO @ Tue, 16 Jun 2020 09:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.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 09:02:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:19: 6000000 INFO @ Tue, 16 Jun 2020 09:02:21: 12000000 INFO @ Tue, 16 Jun 2020 09:02:21: 1000000 INFO @ Tue, 16 Jun 2020 09:02:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:22: #1 total tags in treatment: 4034098 INFO @ Tue, 16 Jun 2020 09:02:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:22: #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 09:02:22: #1 tags after filtering in treatment: 3822936 INFO @ Tue, 16 Jun 2020 09:02:22: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 16 Jun 2020 09:02:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:23: #2 number of paired peaks: 339 WARNING @ Tue, 16 Jun 2020 09:02:23: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:23: #2 predicted fragment length is 138 bps INFO @ Tue, 16 Jun 2020 09:02:23: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 16 Jun 2020 09:02:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.05_model.r INFO @ Tue, 16 Jun 2020 09:02:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:25: 7000000 INFO @ Tue, 16 Jun 2020 09:02:27: 2000000 INFO @ Tue, 16 Jun 2020 09:02:31: 8000000 INFO @ Tue, 16 Jun 2020 09:02:32: 3000000 INFO @ Tue, 16 Jun 2020 09:02:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:36: 9000000 INFO @ Tue, 16 Jun 2020 09:02:37: 4000000 INFO @ Tue, 16 Jun 2020 09:02:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.05_summits.bed INFO @ Tue, 16 Jun 2020 09:02:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:42: 10000000 INFO @ Tue, 16 Jun 2020 09:02:42: 5000000 INFO @ Tue, 16 Jun 2020 09:02:47: 11000000 INFO @ Tue, 16 Jun 2020 09:02:47: 6000000 INFO @ Tue, 16 Jun 2020 09:02:52: 12000000 INFO @ Tue, 16 Jun 2020 09:02:53: 7000000 INFO @ Tue, 16 Jun 2020 09:02:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:54: #1 total tags in treatment: 4034098 INFO @ Tue, 16 Jun 2020 09:02:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:54: #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 09:02:54: #1 tags after filtering in treatment: 3822936 INFO @ Tue, 16 Jun 2020 09:02:54: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 16 Jun 2020 09:02:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:54: #2 number of paired peaks: 339 WARNING @ Tue, 16 Jun 2020 09:02:54: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:54: #2 predicted fragment length is 138 bps INFO @ Tue, 16 Jun 2020 09:02:54: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 16 Jun 2020 09:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.10_model.r INFO @ Tue, 16 Jun 2020 09:02:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:58: 8000000 INFO @ Tue, 16 Jun 2020 09:03:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:03: 9000000 INFO @ Tue, 16 Jun 2020 09:03:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.10_summits.bed INFO @ Tue, 16 Jun 2020 09:03:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:08: 10000000 INFO @ Tue, 16 Jun 2020 09:03:13: 11000000 INFO @ Tue, 16 Jun 2020 09:03:19: 12000000 INFO @ Tue, 16 Jun 2020 09:03:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:20: #1 total tags in treatment: 4034098 INFO @ Tue, 16 Jun 2020 09:03:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:20: #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 09:03:20: #1 tags after filtering in treatment: 3822936 INFO @ Tue, 16 Jun 2020 09:03:20: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 16 Jun 2020 09:03:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:20: #2 number of paired peaks: 339 WARNING @ Tue, 16 Jun 2020 09:03:20: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:20: #2 predicted fragment length is 138 bps INFO @ Tue, 16 Jun 2020 09:03:20: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 16 Jun 2020 09:03:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.20_model.r INFO @ Tue, 16 Jun 2020 09:03:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:03:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085391/SRX4085391.20_summits.bed INFO @ Tue, 16 Jun 2020 09:03:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (99 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。