Job ID = 6367548 SRX = SRX331304 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:30:05 prefetch.2.10.7: 1) Downloading 'SRR947541'... 2020-06-15T23:30:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:30:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:30:48 prefetch.2.10.7: 'SRR947541' is valid 2020-06-15T23:30:48 prefetch.2.10.7: 1) 'SRR947541' was downloaded successfully Read 7603807 spots for SRR947541/SRR947541.sra Written 7603807 spots for SRR947541/SRR947541.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: 00:01:14 7603807 reads; of these: 7603807 (100.00%) were unpaired; of these: 826830 (10.87%) aligned 0 times 5493476 (72.25%) aligned exactly 1 time 1283501 (16.88%) aligned >1 times 89.13% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 1068946 / 6776977 = 0.1577 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 08:34:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.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 08:34:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:13: 1000000 INFO @ Tue, 16 Jun 2020 08:34:18: 2000000 INFO @ Tue, 16 Jun 2020 08:34:23: 3000000 INFO @ Tue, 16 Jun 2020 08:34:28: 4000000 INFO @ Tue, 16 Jun 2020 08:34:34: 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 08:34:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:37: #1 total tags in treatment: 5708031 INFO @ Tue, 16 Jun 2020 08:34:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:37: #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 08:34:37: #1 tags after filtering in treatment: 5708031 INFO @ Tue, 16 Jun 2020 08:34:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.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 08:34:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:38: #2 number of paired peaks: 608 WARNING @ Tue, 16 Jun 2020 08:34:38: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:38: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 08:34:38: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 16 Jun 2020 08:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.05_model.r INFO @ Tue, 16 Jun 2020 08:34:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:43: 1000000 INFO @ Tue, 16 Jun 2020 08:34:48: 2000000 INFO @ Tue, 16 Jun 2020 08:34:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:53: 3000000 INFO @ Tue, 16 Jun 2020 08:34:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:58: 4000000 INFO @ Tue, 16 Jun 2020 08:34:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.05_summits.bed INFO @ Tue, 16 Jun 2020 08:34:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2484 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:03: 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 08:35:07: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:07: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:07: #1 total tags in treatment: 5708031 INFO @ Tue, 16 Jun 2020 08:35:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:07: #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 08:35:07: #1 tags after filtering in treatment: 5708031 INFO @ Tue, 16 Jun 2020 08:35:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:07: #2 number of paired peaks: 608 WARNING @ Tue, 16 Jun 2020 08:35:07: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:07: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 08:35:07: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 16 Jun 2020 08:35:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.10_model.r INFO @ Tue, 16 Jun 2020 08:35:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.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 08:35:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:13: 1000000 INFO @ Tue, 16 Jun 2020 08:35:18: 2000000 INFO @ Tue, 16 Jun 2020 08:35:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:23: 3000000 INFO @ Tue, 16 Jun 2020 08:35:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1256 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:28: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:34: 5000000 INFO @ Tue, 16 Jun 2020 08:35:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:37: #1 total tags in treatment: 5708031 INFO @ Tue, 16 Jun 2020 08:35:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:37: #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 08:35:37: #1 tags after filtering in treatment: 5708031 INFO @ Tue, 16 Jun 2020 08:35:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:38: #2 number of paired peaks: 608 WARNING @ Tue, 16 Jun 2020 08:35:38: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:38: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 08:35:38: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 16 Jun 2020 08:35:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.20_model.r INFO @ Tue, 16 Jun 2020 08:35:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:35:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331304/SRX331304.20_summits.bed INFO @ Tue, 16 Jun 2020 08:35:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (471 records, 4 fields): 2 millis CompletedMACS2peakCalling