Job ID = 6367500 SRX = SRX331257 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:35 prefetch.2.10.7: 1) Downloading 'SRR947489'... 2020-06-15T23:31:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:13 prefetch.2.10.7: 'SRR947489' is valid 2020-06-15T23:32:13 prefetch.2.10.7: 1) 'SRR947489' was downloaded successfully Read 7201747 spots for SRR947489/SRR947489.sra Written 7201747 spots for SRR947489/SRR947489.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: 00:01:10 7201747 reads; of these: 7201747 (100.00%) were unpaired; of these: 182340 (2.53%) aligned 0 times 5948501 (82.60%) aligned exactly 1 time 1070906 (14.87%) aligned >1 times 97.47% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 819956 / 7019407 = 0.1168 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 08:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.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 08:35:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:35: 1000000 INFO @ Tue, 16 Jun 2020 08:35:39: 2000000 INFO @ Tue, 16 Jun 2020 08:35:43: 3000000 INFO @ Tue, 16 Jun 2020 08:35:48: 4000000 INFO @ Tue, 16 Jun 2020 08:35:53: 5000000 INFO @ Tue, 16 Jun 2020 08:35:57: 6000000 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 08:35:58: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:58: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:58: #1 total tags in treatment: 6199451 INFO @ Tue, 16 Jun 2020 08:35:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:58: #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 08:35:58: #1 tags after filtering in treatment: 6199451 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 08:35:59: #2 number of paired peaks: 403 WARNING @ Tue, 16 Jun 2020 08:35:59: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:59: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:35:59: #2 alternative fragment length(s) may be 2,30 bps INFO @ Tue, 16 Jun 2020 08:35:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.05_model.r WARNING @ Tue, 16 Jun 2020 08:35:59: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:59: #2 You may need to consider one of the other alternative d(s): 2,30 WARNING @ Tue, 16 Jun 2020 08:35:59: #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 08:35:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.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 08:36:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:05: 1000000 INFO @ Tue, 16 Jun 2020 08:36:10: 2000000 INFO @ Tue, 16 Jun 2020 08:36:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:15: 3000000 INFO @ Tue, 16 Jun 2020 08:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (492 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:20: 4000000 INFO @ Tue, 16 Jun 2020 08:36:25: 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 08:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.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 08:36:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:30: 6000000 INFO @ Tue, 16 Jun 2020 08:36:31: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:31: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:31: #1 total tags in treatment: 6199451 INFO @ Tue, 16 Jun 2020 08:36:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:31: #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 08:36:31: #1 tags after filtering in treatment: 6199451 INFO @ Tue, 16 Jun 2020 08:36:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:32: #2 number of paired peaks: 403 WARNING @ Tue, 16 Jun 2020 08:36:32: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:32: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:36:32: #2 alternative fragment length(s) may be 2,30 bps INFO @ Tue, 16 Jun 2020 08:36:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.10_model.r WARNING @ Tue, 16 Jun 2020 08:36:32: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:32: #2 You may need to consider one of the other alternative d(s): 2,30 WARNING @ Tue, 16 Jun 2020 08:36:32: #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 08:36:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:35: 1000000 INFO @ Tue, 16 Jun 2020 08:36:40: 2000000 INFO @ Tue, 16 Jun 2020 08:36:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:45: 3000000 INFO @ Tue, 16 Jun 2020 08:36:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.10_summits.bed INFO @ Tue, 16 Jun 2020 08:36:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:50: 4000000 INFO @ Tue, 16 Jun 2020 08:36:55: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:00: 6000000 INFO @ Tue, 16 Jun 2020 08:37:01: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:01: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:01: #1 total tags in treatment: 6199451 INFO @ Tue, 16 Jun 2020 08:37:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:01: #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 08:37:01: #1 tags after filtering in treatment: 6199451 INFO @ Tue, 16 Jun 2020 08:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:02: #2 number of paired peaks: 403 WARNING @ Tue, 16 Jun 2020 08:37:02: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:02: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:37:02: #2 alternative fragment length(s) may be 2,30 bps INFO @ Tue, 16 Jun 2020 08:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.20_model.r WARNING @ Tue, 16 Jun 2020 08:37:02: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:02: #2 You may need to consider one of the other alternative d(s): 2,30 WARNING @ Tue, 16 Jun 2020 08:37:02: #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 08:37:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331257/SRX331257.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (57 records, 4 fields): 1 millis CompletedMACS2peakCalling