Job ID = 6367366 SRX = SRX331125 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 'SRR947356'... 2020-06-15T23:32:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:16 prefetch.2.10.7: 'SRR947356' is valid 2020-06-15T23:33:16 prefetch.2.10.7: 1) 'SRR947356' was downloaded successfully Read 8151012 spots for SRR947356/SRR947356.sra Written 8151012 spots for SRR947356/SRR947356.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: 00:01:16 8151012 reads; of these: 8151012 (100.00%) were unpaired; of these: 65794 (0.81%) aligned 0 times 6797322 (83.39%) aligned exactly 1 time 1287896 (15.80%) aligned >1 times 99.19% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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] 838287 / 8085218 = 0.1037 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 08:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.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 08:36:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:55: 1000000 INFO @ Tue, 16 Jun 2020 08:37:01: 2000000 INFO @ Tue, 16 Jun 2020 08:37:07: 3000000 INFO @ Tue, 16 Jun 2020 08:37:12: 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 08:37:18: 5000000 INFO @ Tue, 16 Jun 2020 08:37:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.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 08:37:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:24: 6000000 INFO @ Tue, 16 Jun 2020 08:37:25: 1000000 INFO @ Tue, 16 Jun 2020 08:37:29: 7000000 INFO @ Tue, 16 Jun 2020 08:37:30: 2000000 INFO @ Tue, 16 Jun 2020 08:37:31: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:31: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:31: #1 total tags in treatment: 7246931 INFO @ Tue, 16 Jun 2020 08:37:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:31: #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 08:37:31: #1 tags after filtering in treatment: 7246931 INFO @ Tue, 16 Jun 2020 08:37:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:31: #2 number of paired peaks: 373 WARNING @ Tue, 16 Jun 2020 08:37:31: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:31: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:37:31: #2 alternative fragment length(s) may be 2,31,509,525,545,571 bps INFO @ Tue, 16 Jun 2020 08:37:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.05_model.r WARNING @ Tue, 16 Jun 2020 08:37:31: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:31: #2 You may need to consider one of the other alternative d(s): 2,31,509,525,545,571 WARNING @ Tue, 16 Jun 2020 08:37:31: #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 08:37:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:36: 3000000 INFO @ Tue, 16 Jun 2020 08:37:41: 4000000 INFO @ Tue, 16 Jun 2020 08:37:46: 5000000 INFO @ Tue, 16 Jun 2020 08:37:46: #3 Call peaks for each chromosome... 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 08:37:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.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 08:37:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:51: 6000000 INFO @ Tue, 16 Jun 2020 08:37:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (563 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:54: 1000000 INFO @ Tue, 16 Jun 2020 08:37:57: 7000000 INFO @ Tue, 16 Jun 2020 08:37:58: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:58: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:58: #1 total tags in treatment: 7246931 INFO @ Tue, 16 Jun 2020 08:37:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:58: #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 08:37:58: #1 tags after filtering in treatment: 7246931 INFO @ Tue, 16 Jun 2020 08:37:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:59: #2 number of paired peaks: 373 WARNING @ Tue, 16 Jun 2020 08:37:59: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:59: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:37:59: #2 alternative fragment length(s) may be 2,31,509,525,545,571 bps INFO @ Tue, 16 Jun 2020 08:37:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.10_model.r WARNING @ Tue, 16 Jun 2020 08:37:59: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:59: #2 You may need to consider one of the other alternative d(s): 2,31,509,525,545,571 WARNING @ Tue, 16 Jun 2020 08:37:59: #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 08:37:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:59: 2000000 INFO @ Tue, 16 Jun 2020 08:38:04: 3000000 INFO @ Tue, 16 Jun 2020 08:38:08: 4000000 INFO @ Tue, 16 Jun 2020 08:38:13: 5000000 INFO @ Tue, 16 Jun 2020 08:38:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:18: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:38:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.10_summits.bed INFO @ Tue, 16 Jun 2020 08:38:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:38:22: 7000000 INFO @ Tue, 16 Jun 2020 08:38:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:38:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:38:23: #1 total tags in treatment: 7246931 INFO @ Tue, 16 Jun 2020 08:38:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:23: #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 08:38:24: #1 tags after filtering in treatment: 7246931 INFO @ Tue, 16 Jun 2020 08:38:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:24: #2 number of paired peaks: 373 WARNING @ Tue, 16 Jun 2020 08:38:24: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:24: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:38:24: #2 alternative fragment length(s) may be 2,31,509,525,545,571 bps INFO @ Tue, 16 Jun 2020 08:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.20_model.r WARNING @ Tue, 16 Jun 2020 08:38:24: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:38:24: #2 You may need to consider one of the other alternative d(s): 2,31,509,525,545,571 WARNING @ Tue, 16 Jun 2020 08:38:24: #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 08:38:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:38:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331125/SRX331125.20_summits.bed INFO @ Tue, 16 Jun 2020 08:38:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (70 records, 4 fields): 1 millis CompletedMACS2peakCalling