Job ID = 6497374 SRX = SRX331185 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:29:13 prefetch.2.10.7: 1) Downloading 'SRR947417'... 2020-06-25T22:29:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:29:42 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:29:42 prefetch.2.10.7: 'SRR947417' is valid 2020-06-25T22:29:42 prefetch.2.10.7: 1) 'SRR947417' was downloaded successfully Read 2458175 spots for SRR947417/SRR947417.sra Written 2458175 spots for SRR947417/SRR947417.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: 00:00:27 2458175 reads; of these: 2458175 (100.00%) were unpaired; of these: 35532 (1.45%) aligned 0 times 2037503 (82.89%) aligned exactly 1 time 385140 (15.67%) aligned >1 times 98.55% overall alignment rate Time searching: 00:00:27 Overall time: 00:00:27 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] 136494 / 2422643 = 0.0563 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 @ Fri, 26 Jun 2020 07:31:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.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 @ Fri, 26 Jun 2020 07:31:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:20: 1000000 INFO @ Fri, 26 Jun 2020 07:31:25: 2000000 INFO @ Fri, 26 Jun 2020 07:31:27: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 07:31:27: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 07:31:27: #1 total tags in treatment: 2286149 INFO @ Fri, 26 Jun 2020 07:31:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:31:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:31:27: #1 tags after filtering in treatment: 2286149 INFO @ Fri, 26 Jun 2020 07:31:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:31:27: #1 finished! INFO @ Fri, 26 Jun 2020 07:31:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:31:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:31:27: #2 number of paired peaks: 427 WARNING @ Fri, 26 Jun 2020 07:31:27: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Fri, 26 Jun 2020 07:31:27: start model_add_line... INFO @ Fri, 26 Jun 2020 07:31:27: start X-correlation... INFO @ Fri, 26 Jun 2020 07:31:27: end of X-cor INFO @ Fri, 26 Jun 2020 07:31:27: #2 finished! INFO @ Fri, 26 Jun 2020 07:31:27: #2 predicted fragment length is 32 bps INFO @ Fri, 26 Jun 2020 07:31:27: #2 alternative fragment length(s) may be 32,472 bps INFO @ Fri, 26 Jun 2020 07:31:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.05_model.r WARNING @ Fri, 26 Jun 2020 07:31:27: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:31:27: #2 You may need to consider one of the other alternative d(s): 32,472 WARNING @ Fri, 26 Jun 2020 07:31:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:31:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:31:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:31:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:31:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:31:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:31:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.05_summits.bed INFO @ Fri, 26 Jun 2020 07:31:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (241 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 @ Fri, 26 Jun 2020 07:31:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.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 @ Fri, 26 Jun 2020 07:31:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:50: 1000000 INFO @ Fri, 26 Jun 2020 07:31:56: 2000000 INFO @ Fri, 26 Jun 2020 07:31:57: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 07:31:57: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 07:31:57: #1 total tags in treatment: 2286149 INFO @ Fri, 26 Jun 2020 07:31:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:31:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:31:57: #1 tags after filtering in treatment: 2286149 INFO @ Fri, 26 Jun 2020 07:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:31:57: #1 finished! INFO @ Fri, 26 Jun 2020 07:31:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:31:57: #2 number of paired peaks: 427 WARNING @ Fri, 26 Jun 2020 07:31:57: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Fri, 26 Jun 2020 07:31:57: start model_add_line... INFO @ Fri, 26 Jun 2020 07:31:57: start X-correlation... INFO @ Fri, 26 Jun 2020 07:31:57: end of X-cor INFO @ Fri, 26 Jun 2020 07:31:57: #2 finished! INFO @ Fri, 26 Jun 2020 07:31:57: #2 predicted fragment length is 32 bps INFO @ Fri, 26 Jun 2020 07:31:57: #2 alternative fragment length(s) may be 32,472 bps INFO @ Fri, 26 Jun 2020 07:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.10_model.r WARNING @ Fri, 26 Jun 2020 07:31:57: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:31:57: #2 You may need to consider one of the other alternative d(s): 32,472 WARNING @ Fri, 26 Jun 2020 07:31:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:31:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:32:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:32:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:32:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:32:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.10_summits.bed INFO @ Fri, 26 Jun 2020 07:32:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (92 records, 4 fields): 2 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 @ Fri, 26 Jun 2020 07:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.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 @ Fri, 26 Jun 2020 07:32:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:32:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:32:21: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:32:27: 2000000 INFO @ Fri, 26 Jun 2020 07:32:28: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 07:32:28: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 07:32:28: #1 total tags in treatment: 2286149 INFO @ Fri, 26 Jun 2020 07:32:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:32:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:32:28: #1 tags after filtering in treatment: 2286149 INFO @ Fri, 26 Jun 2020 07:32:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:32:28: #1 finished! INFO @ Fri, 26 Jun 2020 07:32:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:32:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:32:28: #2 number of paired peaks: 427 WARNING @ Fri, 26 Jun 2020 07:32:28: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Fri, 26 Jun 2020 07:32:28: start model_add_line... INFO @ Fri, 26 Jun 2020 07:32:28: start X-correlation... INFO @ Fri, 26 Jun 2020 07:32:28: end of X-cor INFO @ Fri, 26 Jun 2020 07:32:28: #2 finished! INFO @ Fri, 26 Jun 2020 07:32:28: #2 predicted fragment length is 32 bps INFO @ Fri, 26 Jun 2020 07:32:28: #2 alternative fragment length(s) may be 32,472 bps INFO @ Fri, 26 Jun 2020 07:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.20_model.r WARNING @ Fri, 26 Jun 2020 07:32:28: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:32:28: #2 You may need to consider one of the other alternative d(s): 32,472 WARNING @ Fri, 26 Jun 2020 07:32:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:32:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:32:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:32:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331185/SRX331185.20_summits.bed INFO @ Fri, 26 Jun 2020 07:32:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (27 records, 4 fields): 7 millis CompletedMACS2peakCalling