Job ID = 6367335 SRX = SRX331097 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:20 prefetch.2.10.7: 1) Downloading 'SRR947327'... 2020-06-15T23:32:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:53 prefetch.2.10.7: 'SRR947327' is valid 2020-06-15T23:32:53 prefetch.2.10.7: 1) 'SRR947327' was downloaded successfully Read 4979754 spots for SRR947327/SRR947327.sra Written 4979754 spots for SRR947327/SRR947327.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: 00:00:49 4979754 reads; of these: 4979754 (100.00%) were unpaired; of these: 114889 (2.31%) aligned 0 times 4148033 (83.30%) aligned exactly 1 time 716832 (14.39%) aligned >1 times 97.69% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 457750 / 4864865 = 0.0941 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 08:35:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.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 08:35:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:32: 1000000 INFO @ Tue, 16 Jun 2020 08:35:40: 2000000 INFO @ Tue, 16 Jun 2020 08:35:47: 3000000 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 08:35:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.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 08:35:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:55: 4000000 INFO @ Tue, 16 Jun 2020 08:35:57: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:57: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:57: #1 total tags in treatment: 4407115 INFO @ Tue, 16 Jun 2020 08:35:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:57: #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 08:35:58: #1 tags after filtering in treatment: 4407115 INFO @ Tue, 16 Jun 2020 08:35:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:58: #2 number of paired peaks: 377 WARNING @ Tue, 16 Jun 2020 08:35:58: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:58: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:35:58: #2 alternative fragment length(s) may be 2,34 bps INFO @ Tue, 16 Jun 2020 08:35:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.05_model.r WARNING @ Tue, 16 Jun 2020 08:35:58: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:58: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Tue, 16 Jun 2020 08:35:58: #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 08:35:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:00: 1000000 INFO @ Tue, 16 Jun 2020 08:36:07: 2000000 INFO @ Tue, 16 Jun 2020 08:36:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:13: 3000000 INFO @ Tue, 16 Jun 2020 08:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (378 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:19: 4000000 INFO @ Tue, 16 Jun 2020 08:36:21: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:21: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:21: #1 total tags in treatment: 4407115 INFO @ Tue, 16 Jun 2020 08:36:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:21: #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 08:36:21: #1 tags after filtering in treatment: 4407115 INFO @ Tue, 16 Jun 2020 08:36:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:22: #2 number of paired peaks: 377 WARNING @ Tue, 16 Jun 2020 08:36:22: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:22: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:36:22: #2 alternative fragment length(s) may be 2,34 bps INFO @ Tue, 16 Jun 2020 08:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.10_model.r WARNING @ Tue, 16 Jun 2020 08:36:22: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:22: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Tue, 16 Jun 2020 08:36:22: #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 08:36:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:22: #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 08:36:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.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 08:36:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:31: 1000000 INFO @ Tue, 16 Jun 2020 08:36:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.10_summits.bed INFO @ Tue, 16 Jun 2020 08:36:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:38: 2000000 INFO @ Tue, 16 Jun 2020 08:36:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:36:52: 4000000 INFO @ Tue, 16 Jun 2020 08:36:55: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:55: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:55: #1 total tags in treatment: 4407115 INFO @ Tue, 16 Jun 2020 08:36:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:55: #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 08:36:55: #1 tags after filtering in treatment: 4407115 INFO @ Tue, 16 Jun 2020 08:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:55: #2 number of paired peaks: 377 WARNING @ Tue, 16 Jun 2020 08:36:55: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:55: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:36:55: #2 alternative fragment length(s) may be 2,34 bps INFO @ Tue, 16 Jun 2020 08:36:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.20_model.r WARNING @ Tue, 16 Jun 2020 08:36:55: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:55: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Tue, 16 Jun 2020 08:36:55: #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 08:36:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331097/SRX331097.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 2 millis CompletedMACS2peakCalling