Job ID = 6367856 SRX = SRX4085424 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:41:44 prefetch.2.10.7: 1) Downloading 'SRR7167453'... 2020-06-15T23:41:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:40 prefetch.2.10.7: 1) 'SRR7167453' was downloaded successfully Read 13497903 spots for SRR7167453/SRR7167453.sra Written 13497903 spots for SRR7167453/SRR7167453.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: 00:07:45 13497903 reads; of these: 13497903 (100.00%) were paired; of these: 10267698 (76.07%) aligned concordantly 0 times 2808931 (20.81%) aligned concordantly exactly 1 time 421274 (3.12%) aligned concordantly >1 times ---- 10267698 pairs aligned concordantly 0 times; of these: 214129 (2.09%) aligned discordantly 1 time ---- 10053569 pairs aligned 0 times concordantly or discordantly; of these: 20107138 mates make up the pairs; of these: 14135904 (70.30%) aligned 0 times 5321216 (26.46%) aligned exactly 1 time 650018 (3.23%) aligned >1 times 47.64% overall alignment rate Time searching: 00:07:45 Overall time: 00:07:45 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] 182754 / 3328487 = 0.0549 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 09:00:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.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 09:00:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:57: 1000000 INFO @ Tue, 16 Jun 2020 09:01:02: 2000000 INFO @ Tue, 16 Jun 2020 09:01:07: 3000000 INFO @ Tue, 16 Jun 2020 09:01:12: 4000000 INFO @ Tue, 16 Jun 2020 09:01:17: 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 09:01:22: 6000000 INFO @ Tue, 16 Jun 2020 09:01:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.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 09:01:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:26: 7000000 INFO @ Tue, 16 Jun 2020 09:01:27: 1000000 INFO @ Tue, 16 Jun 2020 09:01:31: 8000000 INFO @ Tue, 16 Jun 2020 09:01:32: 2000000 INFO @ Tue, 16 Jun 2020 09:01:36: 9000000 INFO @ Tue, 16 Jun 2020 09:01:37: 3000000 INFO @ Tue, 16 Jun 2020 09:01:41: 10000000 INFO @ Tue, 16 Jun 2020 09:01:42: 4000000 INFO @ Tue, 16 Jun 2020 09:01:46: 11000000 INFO @ Tue, 16 Jun 2020 09:01:47: 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 09:01:51: 12000000 INFO @ Tue, 16 Jun 2020 09:01:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.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 09:01:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:52: 6000000 INFO @ Tue, 16 Jun 2020 09:01:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:01:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:01:53: #1 total tags in treatment: 3050683 INFO @ Tue, 16 Jun 2020 09:01:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:53: #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 09:01:53: #1 tags after filtering in treatment: 2866273 INFO @ Tue, 16 Jun 2020 09:01:53: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 09:01:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:53: #2 number of paired peaks: 271 WARNING @ Tue, 16 Jun 2020 09:01:53: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 16 Jun 2020 09:01:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:53: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 09:01:53: #2 alternative fragment length(s) may be 162,559 bps INFO @ Tue, 16 Jun 2020 09:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.05_model.r INFO @ Tue, 16 Jun 2020 09:01:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:57: 1000000 INFO @ Tue, 16 Jun 2020 09:01:57: 7000000 INFO @ Tue, 16 Jun 2020 09:01:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:02: 2000000 INFO @ Tue, 16 Jun 2020 09:02:02: 8000000 INFO @ Tue, 16 Jun 2020 09:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.05_summits.bed INFO @ Tue, 16 Jun 2020 09:02:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (657 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:07: 3000000 INFO @ Tue, 16 Jun 2020 09:02:07: 9000000 INFO @ Tue, 16 Jun 2020 09:02:12: 4000000 INFO @ Tue, 16 Jun 2020 09:02:12: 10000000 INFO @ Tue, 16 Jun 2020 09:02:17: 5000000 INFO @ Tue, 16 Jun 2020 09:02:17: 11000000 INFO @ Tue, 16 Jun 2020 09:02:22: 6000000 INFO @ Tue, 16 Jun 2020 09:02:22: 12000000 INFO @ Tue, 16 Jun 2020 09:02:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:24: #1 total tags in treatment: 3050683 INFO @ Tue, 16 Jun 2020 09:02:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:24: #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 09:02:25: #1 tags after filtering in treatment: 2866273 INFO @ Tue, 16 Jun 2020 09:02:25: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 09:02:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:25: #2 number of paired peaks: 271 WARNING @ Tue, 16 Jun 2020 09:02:25: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:25: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 09:02:25: #2 alternative fragment length(s) may be 162,559 bps INFO @ Tue, 16 Jun 2020 09:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.10_model.r INFO @ Tue, 16 Jun 2020 09:02:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:27: 7000000 INFO @ Tue, 16 Jun 2020 09:02:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:32: 8000000 INFO @ Tue, 16 Jun 2020 09:02:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.10_summits.bed INFO @ Tue, 16 Jun 2020 09:02:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:37: 9000000 INFO @ Tue, 16 Jun 2020 09:02:42: 10000000 INFO @ Tue, 16 Jun 2020 09:02:47: 11000000 INFO @ Tue, 16 Jun 2020 09:02:52: 12000000 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: 3050683 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: 2866273 INFO @ Tue, 16 Jun 2020 09:02:54: #1 Redundant rate of treatment: 0.06 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 09:02:55: #2 number of paired peaks: 271 WARNING @ Tue, 16 Jun 2020 09:02:55: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:55: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 09:02:55: #2 alternative fragment length(s) may be 162,559 bps INFO @ Tue, 16 Jun 2020 09:02:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.20_model.r INFO @ Tue, 16 Jun 2020 09:02:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:03:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085424/SRX4085424.20_summits.bed INFO @ Tue, 16 Jun 2020 09:03:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (68 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。