Job ID = 6367814 SRX = SRX4085382 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:51:03 prefetch.2.10.7: 1) Downloading 'SRR7167411'... 2020-06-15T23:51:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:55:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:55:04 prefetch.2.10.7: 1) 'SRR7167411' was downloaded successfully Read 9786578 spots for SRR7167411/SRR7167411.sra Written 9786578 spots for SRR7167411/SRR7167411.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: 00:04:36 9786578 reads; of these: 9786578 (100.00%) were paired; of these: 8215615 (83.95%) aligned concordantly 0 times 1346551 (13.76%) aligned concordantly exactly 1 time 224412 (2.29%) aligned concordantly >1 times ---- 8215615 pairs aligned concordantly 0 times; of these: 238527 (2.90%) aligned discordantly 1 time ---- 7977088 pairs aligned 0 times concordantly or discordantly; of these: 15954176 mates make up the pairs; of these: 11856760 (74.32%) aligned 0 times 3567161 (22.36%) aligned exactly 1 time 530255 (3.32%) aligned >1 times 39.42% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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_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] 101163 / 1680925 = 0.0602 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 09:03:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.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 09:03:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:03:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:03:27: 1000000 INFO @ Tue, 16 Jun 2020 09:03:32: 2000000 INFO @ Tue, 16 Jun 2020 09:03:37: 3000000 INFO @ Tue, 16 Jun 2020 09:03:41: 4000000 INFO @ Tue, 16 Jun 2020 09:03:46: 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 09:03:51: 6000000 INFO @ Tue, 16 Jun 2020 09:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.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 09:03:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:03:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:03:56: 7000000 INFO @ Tue, 16 Jun 2020 09:03:57: 1000000 INFO @ Tue, 16 Jun 2020 09:03:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:58: #1 total tags in treatment: 1475798 INFO @ Tue, 16 Jun 2020 09:03:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:58: #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 09:03:59: #1 tags after filtering in treatment: 1432507 INFO @ Tue, 16 Jun 2020 09:03:59: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 16 Jun 2020 09:03:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:59: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:03:59: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:59: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 09:03:59: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 09:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.05_model.r INFO @ Tue, 16 Jun 2020 09:03:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:04:02: 2000000 INFO @ Tue, 16 Jun 2020 09:04:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.05_summits.bed INFO @ Tue, 16 Jun 2020 09:04:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:04:07: 3000000 INFO @ Tue, 16 Jun 2020 09:04:12: 4000000 INFO @ Tue, 16 Jun 2020 09:04:16: 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 09:04:22: 6000000 INFO @ Tue, 16 Jun 2020 09:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.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 09:04:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:27: 7000000 INFO @ Tue, 16 Jun 2020 09:04:28: 1000000 INFO @ Tue, 16 Jun 2020 09:04:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:04:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:04:29: #1 total tags in treatment: 1475798 INFO @ Tue, 16 Jun 2020 09:04:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:04:29: #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 09:04:29: #1 tags after filtering in treatment: 1432507 INFO @ Tue, 16 Jun 2020 09:04:29: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 16 Jun 2020 09:04:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:04:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:04:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:04:29: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:04:29: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:04:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:04:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:04:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:04:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:04:29: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 09:04:29: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 09:04:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.10_model.r INFO @ Tue, 16 Jun 2020 09:04:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:04:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:33: 2000000 INFO @ Tue, 16 Jun 2020 09:04:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.10_summits.bed INFO @ Tue, 16 Jun 2020 09:04:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (108 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:04:38: 3000000 INFO @ Tue, 16 Jun 2020 09:04:43: 4000000 INFO @ Tue, 16 Jun 2020 09:04:48: 5000000 INFO @ Tue, 16 Jun 2020 09:04:53: 6000000 INFO @ Tue, 16 Jun 2020 09:04:59: 7000000 INFO @ Tue, 16 Jun 2020 09:05:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:05:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:05:02: #1 total tags in treatment: 1475798 INFO @ Tue, 16 Jun 2020 09:05:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:02: #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 09:05:02: #1 tags after filtering in treatment: 1432507 INFO @ Tue, 16 Jun 2020 09:05:02: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 16 Jun 2020 09:05:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:02: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:05:02: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:05:02: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:02: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 09:05:02: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 09:05:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.20_model.r INFO @ Tue, 16 Jun 2020 09:05:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:05:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:05:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:05:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085382/SRX4085382.20_summits.bed INFO @ Tue, 16 Jun 2020 09:05:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (43 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。