Job ID = 14160684 SRX = SRX10399008 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: 00:02:06 10237567 reads; of these: 10237567 (100.00%) were unpaired; of these: 101101 (0.99%) aligned 0 times 8414078 (82.19%) aligned exactly 1 time 1722388 (16.82%) aligned >1 times 99.01% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 742171 / 10136466 = 0.0732 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 03:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.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 03:48:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:48:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:48:50: 1000000 INFO @ Thu, 09 Dec 2021 03:48:56: 2000000 INFO @ Thu, 09 Dec 2021 03:49:03: 3000000 INFO @ Thu, 09 Dec 2021 03:49:09: 4000000 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 03:49:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.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 03:49:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:49:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:49:16: 5000000 INFO @ Thu, 09 Dec 2021 03:49:20: 1000000 INFO @ Thu, 09 Dec 2021 03:49:22: 6000000 INFO @ Thu, 09 Dec 2021 03:49:26: 2000000 INFO @ Thu, 09 Dec 2021 03:49:29: 7000000 INFO @ Thu, 09 Dec 2021 03:49:32: 3000000 INFO @ Thu, 09 Dec 2021 03:49:36: 8000000 INFO @ Thu, 09 Dec 2021 03:49:38: 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 03:49:42: 9000000 INFO @ Thu, 09 Dec 2021 03:49:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.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 03:49:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:49:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:49:45: 5000000 INFO @ Thu, 09 Dec 2021 03:49:45: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:49:45: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:49:45: #1 total tags in treatment: 9394295 INFO @ Thu, 09 Dec 2021 03:49:45: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:49:45: #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 03:49:45: #1 tags after filtering in treatment: 9394295 INFO @ Thu, 09 Dec 2021 03:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:49:45: #1 finished! INFO @ Thu, 09 Dec 2021 03:49:45: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:49:46: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:49:46: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 03:49:46: start model_add_line... INFO @ Thu, 09 Dec 2021 03:49:46: start X-correlation... INFO @ Thu, 09 Dec 2021 03:49:46: end of X-cor INFO @ Thu, 09 Dec 2021 03:49:46: #2 finished! INFO @ Thu, 09 Dec 2021 03:49:46: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 03:49:46: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 03:49:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.05_model.r WARNING @ Thu, 09 Dec 2021 03:49:46: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:49:46: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 03:49:46: #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 03:49:46: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:49:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:49:50: 1000000 INFO @ Thu, 09 Dec 2021 03:49:51: 6000000 INFO @ Thu, 09 Dec 2021 03:49:56: 2000000 INFO @ Thu, 09 Dec 2021 03:49:57: 7000000 INFO @ Thu, 09 Dec 2021 03:50:02: 3000000 INFO @ Thu, 09 Dec 2021 03:50:03: 8000000 INFO @ Thu, 09 Dec 2021 03:50:03: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:50:08: 4000000 INFO @ Thu, 09 Dec 2021 03:50:09: 9000000 INFO @ Thu, 09 Dec 2021 03:50:11: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:50:11: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:50:11: #1 total tags in treatment: 9394295 INFO @ Thu, 09 Dec 2021 03:50:11: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:50:11: #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 03:50:11: #1 tags after filtering in treatment: 9394295 INFO @ Thu, 09 Dec 2021 03:50:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:50:11: #1 finished! INFO @ Thu, 09 Dec 2021 03:50:11: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.05_summits.bed INFO @ Thu, 09 Dec 2021 03:50:12: Done! INFO @ Thu, 09 Dec 2021 03:50:12: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:50:12: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 03:50:12: start model_add_line... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (553 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:50:12: start X-correlation... INFO @ Thu, 09 Dec 2021 03:50:12: end of X-cor INFO @ Thu, 09 Dec 2021 03:50:12: #2 finished! INFO @ Thu, 09 Dec 2021 03:50:12: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 03:50:12: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 03:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.10_model.r WARNING @ Thu, 09 Dec 2021 03:50:12: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:50:12: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 03:50:12: #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 03:50:12: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:50:14: 5000000 INFO @ Thu, 09 Dec 2021 03:50:19: 6000000 INFO @ Thu, 09 Dec 2021 03:50:24: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:50:30: 8000000 INFO @ Thu, 09 Dec 2021 03:50:30: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:50:35: 9000000 INFO @ Thu, 09 Dec 2021 03:50:37: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:50:37: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:50:37: #1 total tags in treatment: 9394295 INFO @ Thu, 09 Dec 2021 03:50:37: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:50:37: #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 03:50:37: #1 tags after filtering in treatment: 9394295 INFO @ Thu, 09 Dec 2021 03:50:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:50:37: #1 finished! INFO @ Thu, 09 Dec 2021 03:50:37: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:50:38: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:50:38: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 03:50:38: start model_add_line... INFO @ Thu, 09 Dec 2021 03:50:38: start X-correlation... INFO @ Thu, 09 Dec 2021 03:50:38: end of X-cor INFO @ Thu, 09 Dec 2021 03:50:38: #2 finished! INFO @ Thu, 09 Dec 2021 03:50:38: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 03:50:38: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 03:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.20_model.r WARNING @ Thu, 09 Dec 2021 03:50:38: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:50:38: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 03:50:38: #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 03:50:38: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.10_summits.bed INFO @ Thu, 09 Dec 2021 03:50:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:50:56: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:51:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:51:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:51:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399008/SRX10399008.20_summits.bed INFO @ Thu, 09 Dec 2021 03:51:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 16 millis CompletedMACS2peakCalling