Job ID = 6367866 SRX = SRX4085433 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:42:29 prefetch.2.10.7: 1) Downloading 'SRR7167462'... 2020-06-15T23:42:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:44:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:44:30 prefetch.2.10.7: 'SRR7167462' is valid 2020-06-15T23:44:30 prefetch.2.10.7: 1) 'SRR7167462' was downloaded successfully Read 5047183 spots for SRR7167462/SRR7167462.sra Written 5047183 spots for SRR7167462/SRR7167462.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: 00:04:03 5047183 reads; of these: 5047183 (100.00%) were paired; of these: 968503 (19.19%) aligned concordantly 0 times 3546103 (70.26%) aligned concordantly exactly 1 time 532577 (10.55%) aligned concordantly >1 times ---- 968503 pairs aligned concordantly 0 times; of these: 160597 (16.58%) aligned discordantly 1 time ---- 807906 pairs aligned 0 times concordantly or discordantly; of these: 1615812 mates make up the pairs; of these: 979171 (60.60%) aligned 0 times 478166 (29.59%) aligned exactly 1 time 158475 (9.81%) aligned >1 times 90.30% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 860987 / 4135403 = 0.2082 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 08:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.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 08:51:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:01: 1000000 INFO @ Tue, 16 Jun 2020 08:52:06: 2000000 INFO @ Tue, 16 Jun 2020 08:52:12: 3000000 INFO @ Tue, 16 Jun 2020 08:52:17: 4000000 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 08:52:23: 5000000 INFO @ Tue, 16 Jun 2020 08:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.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 08:52:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:29: 6000000 INFO @ Tue, 16 Jun 2020 08:52:31: 1000000 INFO @ Tue, 16 Jun 2020 08:52:36: 7000000 INFO @ Tue, 16 Jun 2020 08:52:38: 2000000 INFO @ Tue, 16 Jun 2020 08:52:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:52:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:52:38: #1 total tags in treatment: 3228419 INFO @ Tue, 16 Jun 2020 08:52:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:38: #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 08:52:38: #1 tags after filtering in treatment: 3066869 INFO @ Tue, 16 Jun 2020 08:52:38: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 16 Jun 2020 08:52:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:52:38: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:52:38: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:52:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:38: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 08:52:38: #2 alternative fragment length(s) may be 127,151 bps INFO @ Tue, 16 Jun 2020 08:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.05_model.r INFO @ Tue, 16 Jun 2020 08:52:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:52:43: 3000000 INFO @ Tue, 16 Jun 2020 08:52:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.05_summits.bed INFO @ Tue, 16 Jun 2020 08:52:49: Done! INFO @ Tue, 16 Jun 2020 08:52:49: 4000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (205 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:52:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.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 08:52:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:55: 5000000 INFO @ Tue, 16 Jun 2020 08:53:02: 1000000 INFO @ Tue, 16 Jun 2020 08:53:02: 6000000 INFO @ Tue, 16 Jun 2020 08:53:09: 2000000 INFO @ Tue, 16 Jun 2020 08:53:09: 7000000 INFO @ Tue, 16 Jun 2020 08:53:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:53:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:53:12: #1 total tags in treatment: 3228419 INFO @ Tue, 16 Jun 2020 08:53:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:12: #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 08:53:12: #1 tags after filtering in treatment: 3066869 INFO @ Tue, 16 Jun 2020 08:53:12: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 16 Jun 2020 08:53:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:12: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:53:12: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:12: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 08:53:12: #2 alternative fragment length(s) may be 127,151 bps INFO @ Tue, 16 Jun 2020 08:53:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.10_model.r INFO @ Tue, 16 Jun 2020 08:53:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:53:16: 3000000 INFO @ Tue, 16 Jun 2020 08:53:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:22: 4000000 INFO @ Tue, 16 Jun 2020 08:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.10_summits.bed INFO @ Tue, 16 Jun 2020 08:53:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (151 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:53:29: 5000000 INFO @ Tue, 16 Jun 2020 08:53:35: 6000000 INFO @ Tue, 16 Jun 2020 08:53:42: 7000000 INFO @ Tue, 16 Jun 2020 08:53:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:53:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:53:44: #1 total tags in treatment: 3228419 INFO @ Tue, 16 Jun 2020 08:53:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:44: #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 08:53:44: #1 tags after filtering in treatment: 3066869 INFO @ Tue, 16 Jun 2020 08:53:44: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 16 Jun 2020 08:53:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:45: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:53:45: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:45: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 08:53:45: #2 alternative fragment length(s) may be 127,151 bps INFO @ Tue, 16 Jun 2020 08:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.20_model.r INFO @ Tue, 16 Jun 2020 08:53:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:53:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085433/SRX4085433.20_summits.bed INFO @ Tue, 16 Jun 2020 08:53:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 1 millis CompletedMACS2peakCalling