Job ID = 6365914 SRX = SRX043847 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:23:14 prefetch.2.10.7: 1) Downloading 'SRR107302'... 2020-06-15T22:23:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:23:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:23:43 prefetch.2.10.7: 'SRR107302' is valid 2020-06-15T22:23:43 prefetch.2.10.7: 1) 'SRR107302' was downloaded successfully Read 4420329 spots for SRR107302/SRR107302.sra Written 4420329 spots for SRR107302/SRR107302.sra 2020-06-15T22:24:06 prefetch.2.10.7: 1) Downloading 'SRR107303'... 2020-06-15T22:24:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:24:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:24:36 prefetch.2.10.7: 'SRR107303' is valid 2020-06-15T22:24:36 prefetch.2.10.7: 1) 'SRR107303' was downloaded successfully Read 4223989 spots for SRR107303/SRR107303.sra Written 4223989 spots for SRR107303/SRR107303.sra 2020-06-15T22:24:59 prefetch.2.10.7: 1) Downloading 'SRR107304'... 2020-06-15T22:24:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:25:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:25:19 prefetch.2.10.7: 'SRR107304' is valid 2020-06-15T22:25:19 prefetch.2.10.7: 1) 'SRR107304' was downloaded successfully Read 3083753 spots for SRR107304/SRR107304.sra Written 3083753 spots for SRR107304/SRR107304.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: 00:01:03 11728071 reads; of these: 11728071 (100.00%) were unpaired; of these: 9552031 (81.45%) aligned 0 times 1903467 (16.23%) aligned exactly 1 time 272573 (2.32%) aligned >1 times 18.55% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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_rmdupse_core] 105043 / 2176040 = 0.0483 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 07:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.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 07:27:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:27:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:27:55: 1000000 INFO @ Tue, 16 Jun 2020 07:28:01: 2000000 INFO @ Tue, 16 Jun 2020 07:28:01: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:28:01: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:28:01: #1 total tags in treatment: 2070997 INFO @ Tue, 16 Jun 2020 07:28:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:28:01: #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 07:28:01: #1 tags after filtering in treatment: 2070997 INFO @ Tue, 16 Jun 2020 07:28:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:28:01: #1 finished! INFO @ Tue, 16 Jun 2020 07:28:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:28:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:28:02: #2 number of paired peaks: 282 WARNING @ Tue, 16 Jun 2020 07:28:02: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Tue, 16 Jun 2020 07:28:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:28:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:28:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:28:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:28:02: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:28:02: #2 alternative fragment length(s) may be 39,81,561,583,586 bps INFO @ Tue, 16 Jun 2020 07:28:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.05_model.r WARNING @ Tue, 16 Jun 2020 07:28:02: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:28:02: #2 You may need to consider one of the other alternative d(s): 39,81,561,583,586 WARNING @ Tue, 16 Jun 2020 07:28:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:28:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:28:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:28:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:28:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.05_summits.bed INFO @ Tue, 16 Jun 2020 07:28:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (149 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:28:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.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 07:28:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:28:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:28:26: 1000000 INFO @ Tue, 16 Jun 2020 07:28:32: 2000000 INFO @ Tue, 16 Jun 2020 07:28:33: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:28:33: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:28:33: #1 total tags in treatment: 2070997 INFO @ Tue, 16 Jun 2020 07:28:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:28:33: #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 07:28:33: #1 tags after filtering in treatment: 2070997 INFO @ Tue, 16 Jun 2020 07:28:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:28:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:28:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:28:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:28:33: #2 number of paired peaks: 282 WARNING @ Tue, 16 Jun 2020 07:28:33: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Tue, 16 Jun 2020 07:28:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:28:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:28:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:28:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:28:33: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:28:33: #2 alternative fragment length(s) may be 39,81,561,583,586 bps INFO @ Tue, 16 Jun 2020 07:28:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.10_model.r WARNING @ Tue, 16 Jun 2020 07:28:33: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:28:33: #2 You may need to consider one of the other alternative d(s): 39,81,561,583,586 WARNING @ Tue, 16 Jun 2020 07:28:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:28:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:28:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:28:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:28:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.10_summits.bed INFO @ Tue, 16 Jun 2020 07:28:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (44 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 07:28:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.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 07:28:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:28:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:28:56: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:29:01: 2000000 INFO @ Tue, 16 Jun 2020 07:29:02: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:29:02: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:29:02: #1 total tags in treatment: 2070997 INFO @ Tue, 16 Jun 2020 07:29:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:29:02: #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 07:29:02: #1 tags after filtering in treatment: 2070997 INFO @ Tue, 16 Jun 2020 07:29:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:29:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:29:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:29:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:29:02: #2 number of paired peaks: 282 WARNING @ Tue, 16 Jun 2020 07:29:02: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Tue, 16 Jun 2020 07:29:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:29:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:29:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:29:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:29:02: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:29:02: #2 alternative fragment length(s) may be 39,81,561,583,586 bps INFO @ Tue, 16 Jun 2020 07:29:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.20_model.r WARNING @ Tue, 16 Jun 2020 07:29:02: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:29:02: #2 You may need to consider one of the other alternative d(s): 39,81,561,583,586 WARNING @ Tue, 16 Jun 2020 07:29:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:29:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:29:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:29:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:29:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:29:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:29:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043847/SRX043847.20_summits.bed INFO @ Tue, 16 Jun 2020 07:29:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling