Job ID = 6369038 SRX = SRX982102 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:56:56 prefetch.2.10.7: 1) Downloading 'SRR1956589'... 2020-06-16T00:56:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:57:38 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:57:39 prefetch.2.10.7: 'SRR1956589' is valid 2020-06-16T00:57:39 prefetch.2.10.7: 1) 'SRR1956589' was downloaded successfully Read 6259067 spots for SRR1956589/SRR1956589.sra Written 6259067 spots for SRR1956589/SRR1956589.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: 00:01:18 6259067 reads; of these: 6259067 (100.00%) were unpaired; of these: 291231 (4.65%) aligned 0 times 5049837 (80.68%) aligned exactly 1 time 917999 (14.67%) aligned >1 times 95.35% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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] 274485 / 5967836 = 0.0460 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 10:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.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 10:01:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:01:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:01:55: 1000000 INFO @ Tue, 16 Jun 2020 10:02:00: 2000000 INFO @ Tue, 16 Jun 2020 10:02:05: 3000000 INFO @ Tue, 16 Jun 2020 10:02:09: 4000000 INFO @ Tue, 16 Jun 2020 10:02:14: 5000000 INFO @ Tue, 16 Jun 2020 10:02:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:02:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:02:18: #1 total tags in treatment: 5693351 INFO @ Tue, 16 Jun 2020 10:02:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:02:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 10:02:18: #1 tags after filtering in treatment: 5693351 INFO @ Tue, 16 Jun 2020 10:02:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:02:18: #1 finished! INFO @ Tue, 16 Jun 2020 10:02:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:02:18: #2 number of paired peaks: 310 WARNING @ Tue, 16 Jun 2020 10:02:18: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Tue, 16 Jun 2020 10:02:18: start model_add_line... INFO @ Tue, 16 Jun 2020 10:02:18: start X-correlation... INFO @ Tue, 16 Jun 2020 10:02:18: end of X-cor INFO @ Tue, 16 Jun 2020 10:02:18: #2 finished! INFO @ Tue, 16 Jun 2020 10:02:18: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 10:02:18: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 10:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.05_model.r WARNING @ Tue, 16 Jun 2020 10:02:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:02:18: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 10:02:18: #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 10:02:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.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 10:02:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:26: 1000000 INFO @ Tue, 16 Jun 2020 10:02:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:02:31: 2000000 INFO @ Tue, 16 Jun 2020 10:02:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.05_summits.bed INFO @ Tue, 16 Jun 2020 10:02:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:02:37: 3000000 INFO @ Tue, 16 Jun 2020 10:02:42: 4000000 INFO @ Tue, 16 Jun 2020 10:02:47: 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 10:02:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.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 10:02:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:02:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:02:51: #1 total tags in treatment: 5693351 INFO @ Tue, 16 Jun 2020 10:02:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:02:51: #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 10:02:51: #1 tags after filtering in treatment: 5693351 INFO @ Tue, 16 Jun 2020 10:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:02:51: #1 finished! INFO @ Tue, 16 Jun 2020 10:02:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:02:52: #2 number of paired peaks: 310 WARNING @ Tue, 16 Jun 2020 10:02:52: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Tue, 16 Jun 2020 10:02:52: start model_add_line... INFO @ Tue, 16 Jun 2020 10:02:52: start X-correlation... INFO @ Tue, 16 Jun 2020 10:02:52: end of X-cor INFO @ Tue, 16 Jun 2020 10:02:52: #2 finished! INFO @ Tue, 16 Jun 2020 10:02:52: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 10:02:52: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 10:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.10_model.r WARNING @ Tue, 16 Jun 2020 10:02:52: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:02:52: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 10:02:52: #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 10:02:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:55: 1000000 INFO @ Tue, 16 Jun 2020 10:03:00: 2000000 INFO @ Tue, 16 Jun 2020 10:03:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:03:05: 3000000 INFO @ Tue, 16 Jun 2020 10:03:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.10_summits.bed INFO @ Tue, 16 Jun 2020 10:03:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:03:10: 4000000 INFO @ Tue, 16 Jun 2020 10:03:15: 5000000 INFO @ Tue, 16 Jun 2020 10:03:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:03:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:03:18: #1 total tags in treatment: 5693351 INFO @ Tue, 16 Jun 2020 10:03:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:03:18: #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 10:03:18: #1 tags after filtering in treatment: 5693351 INFO @ Tue, 16 Jun 2020 10:03:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:03:18: #1 finished! INFO @ Tue, 16 Jun 2020 10:03:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:03:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:03:19: #2 number of paired peaks: 310 WARNING @ Tue, 16 Jun 2020 10:03:19: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Tue, 16 Jun 2020 10:03:19: start model_add_line... INFO @ Tue, 16 Jun 2020 10:03:19: start X-correlation... INFO @ Tue, 16 Jun 2020 10:03:19: end of X-cor INFO @ Tue, 16 Jun 2020 10:03:19: #2 finished! INFO @ Tue, 16 Jun 2020 10:03:19: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 10:03:19: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 10:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.20_model.r WARNING @ Tue, 16 Jun 2020 10:03:19: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:03:19: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 10:03:19: #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 10:03:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:03:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:03:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:03:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982102/SRX982102.20_summits.bed INFO @ Tue, 16 Jun 2020 10:03:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (103 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。