Job ID = 6367038 SRX = SRX2761383 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:11:46 prefetch.2.10.7: 1) Downloading 'SRR5476957'... 2020-06-15T23:11:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:09 prefetch.2.10.7: 'SRR5476957' is valid 2020-06-15T23:13:09 prefetch.2.10.7: 1) 'SRR5476957' was downloaded successfully Read 9791265 spots for SRR5476957/SRR5476957.sra Written 9791265 spots for SRR5476957/SRR5476957.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: 00:02:28 9791265 reads; of these: 9791265 (100.00%) were unpaired; of these: 550472 (5.62%) aligned 0 times 6962859 (71.11%) aligned exactly 1 time 2277934 (23.26%) aligned >1 times 94.38% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 1482300 / 9240793 = 0.1604 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 08:18:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.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 08:18:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:58: 1000000 INFO @ Tue, 16 Jun 2020 08:19:04: 2000000 INFO @ Tue, 16 Jun 2020 08:19:11: 3000000 INFO @ Tue, 16 Jun 2020 08:19:17: 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 08:19:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.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 08:19:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:24: 5000000 INFO @ Tue, 16 Jun 2020 08:19:28: 1000000 INFO @ Tue, 16 Jun 2020 08:19:31: 6000000 INFO @ Tue, 16 Jun 2020 08:19:35: 2000000 INFO @ Tue, 16 Jun 2020 08:19:38: 7000000 INFO @ Tue, 16 Jun 2020 08:19:42: 3000000 INFO @ Tue, 16 Jun 2020 08:19:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:19:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:19:43: #1 total tags in treatment: 7758493 INFO @ Tue, 16 Jun 2020 08:19:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:43: #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 08:19:43: #1 tags after filtering in treatment: 7758493 INFO @ Tue, 16 Jun 2020 08:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:44: #2 number of paired peaks: 673 WARNING @ Tue, 16 Jun 2020 08:19:44: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:44: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:19:44: #2 alternative fragment length(s) may be 3,52,565 bps INFO @ Tue, 16 Jun 2020 08:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.05_model.r WARNING @ Tue, 16 Jun 2020 08:19:44: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:44: #2 You may need to consider one of the other alternative d(s): 3,52,565 WARNING @ Tue, 16 Jun 2020 08:19:44: #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 08:19:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:44: #3 Pre-compute pvalue-qvalue table... 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 08:19:49: 4000000 INFO @ Tue, 16 Jun 2020 08:19:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.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 08:19:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:56: 5000000 INFO @ Tue, 16 Jun 2020 08:19:58: 1000000 INFO @ Tue, 16 Jun 2020 08:20:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:04: 6000000 INFO @ Tue, 16 Jun 2020 08:20:05: 2000000 INFO @ Tue, 16 Jun 2020 08:20:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (740 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:11: 7000000 INFO @ Tue, 16 Jun 2020 08:20:12: 3000000 INFO @ Tue, 16 Jun 2020 08:20:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:16: #1 total tags in treatment: 7758493 INFO @ Tue, 16 Jun 2020 08:20:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:16: #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 08:20:16: #1 tags after filtering in treatment: 7758493 INFO @ Tue, 16 Jun 2020 08:20:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:17: #2 number of paired peaks: 673 WARNING @ Tue, 16 Jun 2020 08:20:17: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:17: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:20:17: #2 alternative fragment length(s) may be 3,52,565 bps INFO @ Tue, 16 Jun 2020 08:20:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.10_model.r WARNING @ Tue, 16 Jun 2020 08:20:17: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:17: #2 You may need to consider one of the other alternative d(s): 3,52,565 WARNING @ Tue, 16 Jun 2020 08:20:17: #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 08:20:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:19: 4000000 INFO @ Tue, 16 Jun 2020 08:20:26: 5000000 INFO @ Tue, 16 Jun 2020 08:20:33: 6000000 INFO @ Tue, 16 Jun 2020 08:20:34: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:39: 7000000 INFO @ Tue, 16 Jun 2020 08:20:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (448 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:44: #1 total tags in treatment: 7758493 INFO @ Tue, 16 Jun 2020 08:20:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:44: #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 08:20:44: #1 tags after filtering in treatment: 7758493 INFO @ Tue, 16 Jun 2020 08:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:45: #2 number of paired peaks: 673 WARNING @ Tue, 16 Jun 2020 08:20:45: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:45: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:20:45: #2 alternative fragment length(s) may be 3,52,565 bps INFO @ Tue, 16 Jun 2020 08:20:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.20_model.r WARNING @ Tue, 16 Jun 2020 08:20:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:45: #2 You may need to consider one of the other alternative d(s): 3,52,565 WARNING @ Tue, 16 Jun 2020 08:20:45: #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 08:20:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761383/SRX2761383.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:10: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (181 records, 4 fields): 1 millis CompletedMACS2peakCalling