Job ID = 6366890 SRX = SRX2543058 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:08 prefetch.2.10.7: 1) Downloading 'SRR5235994'... 2020-06-15T23:05:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:32 prefetch.2.10.7: 1) 'SRR5235994' was downloaded successfully 2020-06-15T23:06:33 prefetch.2.10.7: 'SRR5235994' has 0 unresolved dependencies Read 19176956 spots for SRR5235994/SRR5235994.sra Written 19176956 spots for SRR5235994/SRR5235994.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: 00:06:20 19176956 reads; of these: 19176956 (100.00%) were unpaired; of these: 3735663 (19.48%) aligned 0 times 12785698 (66.67%) aligned exactly 1 time 2655595 (13.85%) aligned >1 times 80.52% overall alignment rate Time searching: 00:06:20 Overall time: 00:06:20 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5522589 / 15441293 = 0.3577 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 08:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.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 08:17:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:03: 1000000 INFO @ Tue, 16 Jun 2020 08:18:10: 2000000 INFO @ Tue, 16 Jun 2020 08:18:16: 3000000 INFO @ Tue, 16 Jun 2020 08:18:23: 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 08:18:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.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 08:18:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:30: 5000000 INFO @ Tue, 16 Jun 2020 08:18:35: 1000000 INFO @ Tue, 16 Jun 2020 08:18:38: 6000000 INFO @ Tue, 16 Jun 2020 08:18:43: 2000000 INFO @ Tue, 16 Jun 2020 08:18:45: 7000000 INFO @ Tue, 16 Jun 2020 08:18:50: 3000000 INFO @ Tue, 16 Jun 2020 08:18:53: 8000000 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 08:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.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 08:18:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:58: 4000000 INFO @ Tue, 16 Jun 2020 08:19:01: 9000000 INFO @ Tue, 16 Jun 2020 08:19:07: 1000000 INFO @ Tue, 16 Jun 2020 08:19:07: 5000000 INFO @ Tue, 16 Jun 2020 08:19:09: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:19:09: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:19:09: #1 total tags in treatment: 9918704 INFO @ Tue, 16 Jun 2020 08:19:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:09: #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 08:19:09: #1 tags after filtering in treatment: 9918704 INFO @ Tue, 16 Jun 2020 08:19:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:10: #2 number of paired peaks: 402 WARNING @ Tue, 16 Jun 2020 08:19:10: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:10: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 08:19:10: #2 alternative fragment length(s) may be 3,64,574 bps INFO @ Tue, 16 Jun 2020 08:19:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.05_model.r WARNING @ Tue, 16 Jun 2020 08:19:10: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:10: #2 You may need to consider one of the other alternative d(s): 3,64,574 WARNING @ Tue, 16 Jun 2020 08:19:10: #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 08:19:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:15: 6000000 INFO @ Tue, 16 Jun 2020 08:19:17: 2000000 INFO @ Tue, 16 Jun 2020 08:19:24: 7000000 INFO @ Tue, 16 Jun 2020 08:19:27: 3000000 INFO @ Tue, 16 Jun 2020 08:19:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:33: 8000000 INFO @ Tue, 16 Jun 2020 08:19:37: 4000000 INFO @ Tue, 16 Jun 2020 08:19:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.05_summits.bed INFO @ Tue, 16 Jun 2020 08:19:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (902 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:19:42: 9000000 INFO @ Tue, 16 Jun 2020 08:19:46: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:19:50: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:19:50: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:19:50: #1 total tags in treatment: 9918704 INFO @ Tue, 16 Jun 2020 08:19:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:50: #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 08:19:50: #1 tags after filtering in treatment: 9918704 INFO @ Tue, 16 Jun 2020 08:19:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:51: #2 number of paired peaks: 402 WARNING @ Tue, 16 Jun 2020 08:19:51: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:51: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 08:19:51: #2 alternative fragment length(s) may be 3,64,574 bps INFO @ Tue, 16 Jun 2020 08:19:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.10_model.r WARNING @ Tue, 16 Jun 2020 08:19:51: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:51: #2 You may need to consider one of the other alternative d(s): 3,64,574 WARNING @ Tue, 16 Jun 2020 08:19:51: #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 08:19:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:55: 6000000 INFO @ Tue, 16 Jun 2020 08:20:04: 7000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:20:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:12: 8000000 INFO @ Tue, 16 Jun 2020 08:20:21: 9000000 INFO @ Tue, 16 Jun 2020 08:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (474 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:29: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:20:29: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:20:29: #1 total tags in treatment: 9918704 INFO @ Tue, 16 Jun 2020 08:20:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:29: #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 08:20:29: #1 tags after filtering in treatment: 9918704 INFO @ Tue, 16 Jun 2020 08:20:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:29: #2 number of paired peaks: 402 WARNING @ Tue, 16 Jun 2020 08:20:29: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:30: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 08:20:30: #2 alternative fragment length(s) may be 3,64,574 bps INFO @ Tue, 16 Jun 2020 08:20:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.20_model.r WARNING @ Tue, 16 Jun 2020 08:20:30: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:30: #2 You may need to consider one of the other alternative d(s): 3,64,574 WARNING @ Tue, 16 Jun 2020 08:20:30: #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 08:20:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543058/SRX2543058.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling