Job ID = 6366696 SRX = SRX2228852 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:58:08 prefetch.2.10.7: 1) Downloading 'SRR4380308'... 2020-06-15T22:58:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:53 prefetch.2.10.7: 'SRR4380308' is valid 2020-06-15T22:58:53 prefetch.2.10.7: 1) 'SRR4380308' was downloaded successfully Read 8992104 spots for SRR4380308/SRR4380308.sra Written 8992104 spots for SRR4380308/SRR4380308.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: 00:01:22 8992104 reads; of these: 8992104 (100.00%) were unpaired; of these: 572302 (6.36%) aligned 0 times 7118556 (79.16%) aligned exactly 1 time 1301246 (14.47%) aligned >1 times 93.64% overall alignment rate Time searching: 00:01:22 Overall time: 00:01:22 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_rmdupse_core] 949038 / 8419802 = 0.1127 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 08:02:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.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 08:02:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:01: 1000000 INFO @ Tue, 16 Jun 2020 08:03:06: 2000000 INFO @ Tue, 16 Jun 2020 08:03:12: 3000000 INFO @ Tue, 16 Jun 2020 08:03:18: 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 08:03:24: 5000000 INFO @ Tue, 16 Jun 2020 08:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.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 08:03:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:30: 6000000 INFO @ Tue, 16 Jun 2020 08:03:31: 1000000 INFO @ Tue, 16 Jun 2020 08:03:36: 7000000 INFO @ Tue, 16 Jun 2020 08:03:37: 2000000 INFO @ Tue, 16 Jun 2020 08:03:39: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:03:39: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:03:39: #1 total tags in treatment: 7470764 INFO @ Tue, 16 Jun 2020 08:03:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:39: #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 08:03:39: #1 tags after filtering in treatment: 7470764 INFO @ Tue, 16 Jun 2020 08:03:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:40: #2 number of paired peaks: 362 WARNING @ Tue, 16 Jun 2020 08:03:40: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:40: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 08:03:40: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 16 Jun 2020 08:03:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.05_model.r INFO @ Tue, 16 Jun 2020 08:03:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:43: 3000000 INFO @ Tue, 16 Jun 2020 08:03:49: 4000000 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 08:03:54: 5000000 INFO @ Tue, 16 Jun 2020 08:03:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.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 08:03:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:00: 6000000 INFO @ Tue, 16 Jun 2020 08:04:01: 1000000 INFO @ Tue, 16 Jun 2020 08:04:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (861 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:06: 7000000 INFO @ Tue, 16 Jun 2020 08:04:07: 2000000 INFO @ Tue, 16 Jun 2020 08:04:09: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:04:09: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:04:09: #1 total tags in treatment: 7470764 INFO @ Tue, 16 Jun 2020 08:04:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:09: #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 08:04:09: #1 tags after filtering in treatment: 7470764 INFO @ Tue, 16 Jun 2020 08:04:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:10: #2 number of paired peaks: 362 WARNING @ Tue, 16 Jun 2020 08:04:10: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:10: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 08:04:10: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 16 Jun 2020 08:04:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.10_model.r INFO @ Tue, 16 Jun 2020 08:04:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:13: 3000000 INFO @ Tue, 16 Jun 2020 08:04:18: 4000000 INFO @ Tue, 16 Jun 2020 08:04:24: 5000000 INFO @ Tue, 16 Jun 2020 08:04:26: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:04:29: 6000000 INFO @ Tue, 16 Jun 2020 08:04:35: 7000000 INFO @ Tue, 16 Jun 2020 08:04:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (506 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:37: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:04:37: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:04:37: #1 total tags in treatment: 7470764 INFO @ Tue, 16 Jun 2020 08:04:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:37: #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 08:04:37: #1 tags after filtering in treatment: 7470764 INFO @ Tue, 16 Jun 2020 08:04:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:38: #2 number of paired peaks: 362 WARNING @ Tue, 16 Jun 2020 08:04:38: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:38: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 08:04:38: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 16 Jun 2020 08:04:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.20_model.r INFO @ Tue, 16 Jun 2020 08:04:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:04:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228852/SRX2228852.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (249 records, 4 fields): 1 millis CompletedMACS2peakCalling