Job ID = 14160109 SRX = SRX3180779 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: 00:03:43 17772057 reads; of these: 17772057 (100.00%) were unpaired; of these: 488195 (2.75%) aligned 0 times 14360234 (80.80%) aligned exactly 1 time 2923628 (16.45%) aligned >1 times 97.25% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 2839976 / 17283862 = 0.1643 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 00:56:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.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 00:56:46: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:56:46: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:56:51: 1000000 INFO @ Thu, 09 Dec 2021 00:56:56: 2000000 INFO @ Thu, 09 Dec 2021 00:57:01: 3000000 INFO @ Thu, 09 Dec 2021 00:57:06: 4000000 INFO @ Thu, 09 Dec 2021 00:57:11: 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 00:57:16: 6000000 INFO @ Thu, 09 Dec 2021 00:57:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.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 00:57:16: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:57:16: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:57:21: 7000000 INFO @ Thu, 09 Dec 2021 00:57:21: 1000000 INFO @ Thu, 09 Dec 2021 00:57:27: 8000000 INFO @ Thu, 09 Dec 2021 00:57:27: 2000000 INFO @ Thu, 09 Dec 2021 00:57:32: 9000000 INFO @ Thu, 09 Dec 2021 00:57:32: 3000000 INFO @ Thu, 09 Dec 2021 00:57:37: 10000000 INFO @ Thu, 09 Dec 2021 00:57:38: 4000000 INFO @ Thu, 09 Dec 2021 00:57:43: 11000000 INFO @ Thu, 09 Dec 2021 00:57:43: 5000000 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 00:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.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 00:57:46: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:57:46: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:57:48: 12000000 INFO @ Thu, 09 Dec 2021 00:57:49: 6000000 INFO @ Thu, 09 Dec 2021 00:57:52: 1000000 INFO @ Thu, 09 Dec 2021 00:57:54: 13000000 INFO @ Thu, 09 Dec 2021 00:57:54: 7000000 INFO @ Thu, 09 Dec 2021 00:57:59: 2000000 INFO @ Thu, 09 Dec 2021 00:58:00: 14000000 INFO @ Thu, 09 Dec 2021 00:58:00: 8000000 INFO @ Thu, 09 Dec 2021 00:58:02: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:58:02: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:58:02: #1 total tags in treatment: 14443886 INFO @ Thu, 09 Dec 2021 00:58:02: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:58:02: #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 00:58:02: #1 tags after filtering in treatment: 14443886 INFO @ Thu, 09 Dec 2021 00:58:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:58:02: #1 finished! INFO @ Thu, 09 Dec 2021 00:58:02: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:58:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:58:03: #2 number of paired peaks: 325 WARNING @ Thu, 09 Dec 2021 00:58:03: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Thu, 09 Dec 2021 00:58:03: start model_add_line... INFO @ Thu, 09 Dec 2021 00:58:03: start X-correlation... INFO @ Thu, 09 Dec 2021 00:58:03: end of X-cor INFO @ Thu, 09 Dec 2021 00:58:03: #2 finished! INFO @ Thu, 09 Dec 2021 00:58:03: #2 predicted fragment length is 46 bps INFO @ Thu, 09 Dec 2021 00:58:03: #2 alternative fragment length(s) may be 2,46,528,543,564 bps INFO @ Thu, 09 Dec 2021 00:58:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.05_model.r WARNING @ Thu, 09 Dec 2021 00:58:04: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:58:04: #2 You may need to consider one of the other alternative d(s): 2,46,528,543,564 WARNING @ Thu, 09 Dec 2021 00:58:04: #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 00:58:04: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:58:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:58:05: 3000000 INFO @ Thu, 09 Dec 2021 00:58:06: 9000000 INFO @ Thu, 09 Dec 2021 00:58:12: 4000000 INFO @ Thu, 09 Dec 2021 00:58:12: 10000000 INFO @ Thu, 09 Dec 2021 00:58:17: 11000000 INFO @ Thu, 09 Dec 2021 00:58:18: 5000000 INFO @ Thu, 09 Dec 2021 00:58:23: 12000000 INFO @ Thu, 09 Dec 2021 00:58:24: 6000000 INFO @ Thu, 09 Dec 2021 00:58:28: 13000000 INFO @ Thu, 09 Dec 2021 00:58:29: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:58:31: 7000000 INFO @ Thu, 09 Dec 2021 00:58:34: 14000000 INFO @ Thu, 09 Dec 2021 00:58:37: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:58:37: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:58:37: #1 total tags in treatment: 14443886 INFO @ Thu, 09 Dec 2021 00:58:37: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:58:37: #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 00:58:37: #1 tags after filtering in treatment: 14443886 INFO @ Thu, 09 Dec 2021 00:58:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:58:37: #1 finished! INFO @ Thu, 09 Dec 2021 00:58:37: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:58:37: 8000000 INFO @ Thu, 09 Dec 2021 00:58:38: #2 number of paired peaks: 325 WARNING @ Thu, 09 Dec 2021 00:58:38: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Thu, 09 Dec 2021 00:58:38: start model_add_line... INFO @ Thu, 09 Dec 2021 00:58:38: start X-correlation... INFO @ Thu, 09 Dec 2021 00:58:38: end of X-cor INFO @ Thu, 09 Dec 2021 00:58:38: #2 finished! INFO @ Thu, 09 Dec 2021 00:58:38: #2 predicted fragment length is 46 bps INFO @ Thu, 09 Dec 2021 00:58:38: #2 alternative fragment length(s) may be 2,46,528,543,564 bps INFO @ Thu, 09 Dec 2021 00:58:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.10_model.r WARNING @ Thu, 09 Dec 2021 00:58:38: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:58:38: #2 You may need to consider one of the other alternative d(s): 2,46,528,543,564 WARNING @ Thu, 09 Dec 2021 00:58:38: #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 00:58:38: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:58:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:58:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:58:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.05_summits.bed INFO @ Thu, 09 Dec 2021 00:58:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (711 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:58:43: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:58:49: 10000000 INFO @ Thu, 09 Dec 2021 00:58:55: 11000000 INFO @ Thu, 09 Dec 2021 00:59:02: 12000000 INFO @ Thu, 09 Dec 2021 00:59:03: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:59:07: 13000000 INFO @ Thu, 09 Dec 2021 00:59:13: 14000000 INFO @ Thu, 09 Dec 2021 00:59:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:59:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:59:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.10_summits.bed INFO @ Thu, 09 Dec 2021 00:59:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (461 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:59:16: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:59:16: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:59:16: #1 total tags in treatment: 14443886 INFO @ Thu, 09 Dec 2021 00:59:16: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:59:16: #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 00:59:16: #1 tags after filtering in treatment: 14443886 INFO @ Thu, 09 Dec 2021 00:59:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:59:16: #1 finished! INFO @ Thu, 09 Dec 2021 00:59:16: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:59:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:59:17: #2 number of paired peaks: 325 WARNING @ Thu, 09 Dec 2021 00:59:17: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Thu, 09 Dec 2021 00:59:17: start model_add_line... INFO @ Thu, 09 Dec 2021 00:59:17: start X-correlation... INFO @ Thu, 09 Dec 2021 00:59:17: end of X-cor INFO @ Thu, 09 Dec 2021 00:59:17: #2 finished! INFO @ Thu, 09 Dec 2021 00:59:17: #2 predicted fragment length is 46 bps INFO @ Thu, 09 Dec 2021 00:59:17: #2 alternative fragment length(s) may be 2,46,528,543,564 bps INFO @ Thu, 09 Dec 2021 00:59:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.20_model.r WARNING @ Thu, 09 Dec 2021 00:59:17: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:59:17: #2 You may need to consider one of the other alternative d(s): 2,46,528,543,564 WARNING @ Thu, 09 Dec 2021 00:59:17: #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 00:59:17: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:59:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:59:43: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180779/SRX3180779.20_summits.bed INFO @ Thu, 09 Dec 2021 00:59:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (186 records, 4 fields): 1 millis CompletedMACS2peakCalling