Job ID = 14160593 SRX = SRX9904329 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:42 13498162 reads; of these: 13498162 (100.00%) were unpaired; of these: 3010261 (22.30%) aligned 0 times 8769670 (64.97%) aligned exactly 1 time 1718231 (12.73%) aligned >1 times 77.70% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 1090405 / 10487901 = 0.1040 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:25:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.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 @ Thu, 09 Dec 2021 03:25:29: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:25:29: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:25:35: 1000000 INFO @ Thu, 09 Dec 2021 03:25:40: 2000000 INFO @ Thu, 09 Dec 2021 03:25:46: 3000000 INFO @ Thu, 09 Dec 2021 03:25:51: 4000000 INFO @ Thu, 09 Dec 2021 03:25:57: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.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 @ Thu, 09 Dec 2021 03:26:00: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:26:00: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:26:02: 6000000 INFO @ Thu, 09 Dec 2021 03:26:06: 1000000 INFO @ Thu, 09 Dec 2021 03:26:08: 7000000 INFO @ Thu, 09 Dec 2021 03:26:12: 2000000 INFO @ Thu, 09 Dec 2021 03:26:15: 8000000 INFO @ Thu, 09 Dec 2021 03:26:19: 3000000 INFO @ Thu, 09 Dec 2021 03:26:21: 9000000 INFO @ Thu, 09 Dec 2021 03:26:23: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:26:23: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:26:23: #1 total tags in treatment: 9397496 INFO @ Thu, 09 Dec 2021 03:26:23: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:26:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:26:23: #1 tags after filtering in treatment: 9397496 INFO @ Thu, 09 Dec 2021 03:26:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:26:23: #1 finished! INFO @ Thu, 09 Dec 2021 03:26:23: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:26:24: #2 number of paired peaks: 339 WARNING @ Thu, 09 Dec 2021 03:26:24: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Thu, 09 Dec 2021 03:26:24: start model_add_line... INFO @ Thu, 09 Dec 2021 03:26:24: start X-correlation... INFO @ Thu, 09 Dec 2021 03:26:24: end of X-cor INFO @ Thu, 09 Dec 2021 03:26:24: #2 finished! INFO @ Thu, 09 Dec 2021 03:26:24: #2 predicted fragment length is 50 bps INFO @ Thu, 09 Dec 2021 03:26:24: #2 alternative fragment length(s) may be 3,50,517,522 bps INFO @ Thu, 09 Dec 2021 03:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.05_model.r WARNING @ Thu, 09 Dec 2021 03:26:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:26:24: #2 You may need to consider one of the other alternative d(s): 3,50,517,522 WARNING @ Thu, 09 Dec 2021 03:26:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:26:24: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:26:25: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:26:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.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 @ Thu, 09 Dec 2021 03:26:29: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:26:29: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:26:31: 5000000 INFO @ Thu, 09 Dec 2021 03:26:37: 1000000 INFO @ Thu, 09 Dec 2021 03:26:38: 6000000 INFO @ Thu, 09 Dec 2021 03:26:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:26:44: 2000000 INFO @ Thu, 09 Dec 2021 03:26:44: 7000000 INFO @ Thu, 09 Dec 2021 03:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.05_summits.bed INFO @ Thu, 09 Dec 2021 03:26:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (620 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:26:51: 8000000 INFO @ Thu, 09 Dec 2021 03:26:52: 3000000 INFO @ Thu, 09 Dec 2021 03:26:58: 9000000 INFO @ Thu, 09 Dec 2021 03:27:00: 4000000 INFO @ Thu, 09 Dec 2021 03:27:01: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:27:01: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:27:01: #1 total tags in treatment: 9397496 INFO @ Thu, 09 Dec 2021 03:27:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:27:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:27:01: #1 tags after filtering in treatment: 9397496 INFO @ Thu, 09 Dec 2021 03:27:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:27:01: #1 finished! INFO @ Thu, 09 Dec 2021 03:27:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:27:01: #2 number of paired peaks: 339 WARNING @ Thu, 09 Dec 2021 03:27:01: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Thu, 09 Dec 2021 03:27:01: start model_add_line... INFO @ Thu, 09 Dec 2021 03:27:01: start X-correlation... INFO @ Thu, 09 Dec 2021 03:27:01: end of X-cor INFO @ Thu, 09 Dec 2021 03:27:01: #2 finished! INFO @ Thu, 09 Dec 2021 03:27:01: #2 predicted fragment length is 50 bps INFO @ Thu, 09 Dec 2021 03:27:01: #2 alternative fragment length(s) may be 3,50,517,522 bps INFO @ Thu, 09 Dec 2021 03:27:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.10_model.r WARNING @ Thu, 09 Dec 2021 03:27:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:27:01: #2 You may need to consider one of the other alternative d(s): 3,50,517,522 WARNING @ Thu, 09 Dec 2021 03:27:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:27:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:27:06: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:27:13: 6000000 INFO @ Thu, 09 Dec 2021 03:27:19: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:27:20: 7000000 INFO @ Thu, 09 Dec 2021 03:27:27: 8000000 INFO @ Thu, 09 Dec 2021 03:27:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:27:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:27:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.10_summits.bed INFO @ Thu, 09 Dec 2021 03:27:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (407 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:27:34: 9000000 INFO @ Thu, 09 Dec 2021 03:27:37: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:27:37: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:27:37: #1 total tags in treatment: 9397496 INFO @ Thu, 09 Dec 2021 03:27:37: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:27:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:27:37: #1 tags after filtering in treatment: 9397496 INFO @ Thu, 09 Dec 2021 03:27:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:27:37: #1 finished! INFO @ Thu, 09 Dec 2021 03:27:37: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:27:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:27:38: #2 number of paired peaks: 339 WARNING @ Thu, 09 Dec 2021 03:27:38: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Thu, 09 Dec 2021 03:27:38: start model_add_line... INFO @ Thu, 09 Dec 2021 03:27:38: start X-correlation... INFO @ Thu, 09 Dec 2021 03:27:38: end of X-cor INFO @ Thu, 09 Dec 2021 03:27:38: #2 finished! INFO @ Thu, 09 Dec 2021 03:27:38: #2 predicted fragment length is 50 bps INFO @ Thu, 09 Dec 2021 03:27:38: #2 alternative fragment length(s) may be 3,50,517,522 bps INFO @ Thu, 09 Dec 2021 03:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.20_model.r WARNING @ Thu, 09 Dec 2021 03:27:38: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:27:38: #2 You may need to consider one of the other alternative d(s): 3,50,517,522 WARNING @ Thu, 09 Dec 2021 03:27:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:27:38: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:27:56: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:28:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:28:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:28:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9904329/SRX9904329.20_summits.bed INFO @ Thu, 09 Dec 2021 03:28:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (167 records, 4 fields): 119 millis CompletedMACS2peakCalling