Job ID = 6367672 SRX = SRX3862411 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:50 prefetch.2.10.7: 1) Downloading 'SRR6914648'... 2020-06-15T23:31:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:56 prefetch.2.10.7: 'SRR6914648' is valid 2020-06-15T23:33:56 prefetch.2.10.7: 1) 'SRR6914648' was downloaded successfully 2020-06-15T23:33:56 prefetch.2.10.7: 'SRR6914648' has 0 unresolved dependencies Read 14120288 spots for SRR6914648/SRR6914648.sra Written 14120288 spots for SRR6914648/SRR6914648.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: 00:04:39 14120288 reads; of these: 14120288 (100.00%) were unpaired; of these: 817239 (5.79%) aligned 0 times 11159499 (79.03%) aligned exactly 1 time 2143550 (15.18%) aligned >1 times 94.21% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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] 2300723 / 13303049 = 0.1729 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 08:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.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 08:43:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:33: 1000000 INFO @ Tue, 16 Jun 2020 08:43:40: 2000000 INFO @ Tue, 16 Jun 2020 08:43:47: 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 08:43:54: 4000000 INFO @ Tue, 16 Jun 2020 08:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.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 08:43:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:02: 5000000 INFO @ Tue, 16 Jun 2020 08:44:03: 1000000 INFO @ Tue, 16 Jun 2020 08:44:09: 6000000 INFO @ Tue, 16 Jun 2020 08:44:10: 2000000 INFO @ Tue, 16 Jun 2020 08:44:17: 7000000 INFO @ Tue, 16 Jun 2020 08:44:18: 3000000 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 08:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.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 08:44:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:25: 8000000 INFO @ Tue, 16 Jun 2020 08:44:25: 4000000 INFO @ Tue, 16 Jun 2020 08:44:33: 5000000 INFO @ Tue, 16 Jun 2020 08:44:33: 9000000 INFO @ Tue, 16 Jun 2020 08:44:34: 1000000 INFO @ Tue, 16 Jun 2020 08:44:41: 6000000 INFO @ Tue, 16 Jun 2020 08:44:41: 10000000 INFO @ Tue, 16 Jun 2020 08:44:41: 2000000 INFO @ Tue, 16 Jun 2020 08:44:49: 11000000 INFO @ Tue, 16 Jun 2020 08:44:49: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:44:49: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:44:49: #1 total tags in treatment: 11002326 INFO @ Tue, 16 Jun 2020 08:44:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:49: #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 08:44:49: 7000000 INFO @ Tue, 16 Jun 2020 08:44:49: #1 tags after filtering in treatment: 11002326 INFO @ Tue, 16 Jun 2020 08:44:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:49: 3000000 INFO @ Tue, 16 Jun 2020 08:44:50: #2 number of paired peaks: 264 WARNING @ Tue, 16 Jun 2020 08:44:50: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:50: #2 predicted fragment length is 71 bps INFO @ Tue, 16 Jun 2020 08:44:50: #2 alternative fragment length(s) may be 3,71 bps INFO @ Tue, 16 Jun 2020 08:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.05_model.r WARNING @ Tue, 16 Jun 2020 08:44:50: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:50: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Tue, 16 Jun 2020 08:44:50: #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 08:44:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:57: 8000000 INFO @ Tue, 16 Jun 2020 08:44:57: 4000000 INFO @ Tue, 16 Jun 2020 08:45:04: 9000000 INFO @ Tue, 16 Jun 2020 08:45:05: 5000000 INFO @ Tue, 16 Jun 2020 08:45:12: 10000000 INFO @ Tue, 16 Jun 2020 08:45:13: 6000000 INFO @ Tue, 16 Jun 2020 08:45:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:20: 11000000 INFO @ Tue, 16 Jun 2020 08:45:20: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:45:20: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:45:20: #1 total tags in treatment: 11002326 INFO @ Tue, 16 Jun 2020 08:45:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:20: #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 08:45:20: #1 tags after filtering in treatment: 11002326 INFO @ Tue, 16 Jun 2020 08:45:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:20: 7000000 INFO @ Tue, 16 Jun 2020 08:45:21: #2 number of paired peaks: 264 WARNING @ Tue, 16 Jun 2020 08:45:21: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:21: #2 predicted fragment length is 71 bps INFO @ Tue, 16 Jun 2020 08:45:21: #2 alternative fragment length(s) may be 3,71 bps INFO @ Tue, 16 Jun 2020 08:45:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.10_model.r WARNING @ Tue, 16 Jun 2020 08:45:21: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:21: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Tue, 16 Jun 2020 08:45:21: #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 08:45:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.05_summits.bed INFO @ Tue, 16 Jun 2020 08:45:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:45:27: 8000000 INFO @ Tue, 16 Jun 2020 08:45:34: 9000000 INFO @ Tue, 16 Jun 2020 08:45:41: 10000000 INFO @ Tue, 16 Jun 2020 08:45:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:48: 11000000 INFO @ Tue, 16 Jun 2020 08:45:48: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:45:48: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:45:48: #1 total tags in treatment: 11002326 INFO @ Tue, 16 Jun 2020 08:45:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:48: #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 08:45:48: #1 tags after filtering in treatment: 11002326 INFO @ Tue, 16 Jun 2020 08:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:49: #2 number of paired peaks: 264 WARNING @ Tue, 16 Jun 2020 08:45:49: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:49: #2 predicted fragment length is 71 bps INFO @ Tue, 16 Jun 2020 08:45:49: #2 alternative fragment length(s) may be 3,71 bps INFO @ Tue, 16 Jun 2020 08:45:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.20_model.r WARNING @ Tue, 16 Jun 2020 08:45:49: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:49: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Tue, 16 Jun 2020 08:45:49: #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 08:45:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.10_summits.bed INFO @ Tue, 16 Jun 2020 08:45:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (329 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862411/SRX3862411.20_summits.bed INFO @ Tue, 16 Jun 2020 08:46:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling