Job ID = 14520296 SRX = SRX8421789 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4337242 spots for SRR11872082/SRR11872082.sra Written 4337242 spots for SRR11872082/SRR11872082.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: 00:00:59 4337242 reads; of these: 4337242 (100.00%) were unpaired; of these: 198717 (4.58%) aligned 0 times 3412147 (78.67%) aligned exactly 1 time 726378 (16.75%) aligned >1 times 95.42% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 1812931 / 4138525 = 0.4381 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 @ Sat, 15 Jan 2022 18:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 15 Jan 2022 18:54:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:54:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:54:47: 1000000 INFO @ Sat, 15 Jan 2022 18:54:56: 2000000 INFO @ Sat, 15 Jan 2022 18:54:58: #1 tag size is determined as 101 bps INFO @ Sat, 15 Jan 2022 18:54:58: #1 tag size = 101 INFO @ Sat, 15 Jan 2022 18:54:58: #1 total tags in treatment: 2325594 INFO @ Sat, 15 Jan 2022 18:54:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:54:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:54:58: #1 tags after filtering in treatment: 2325594 INFO @ Sat, 15 Jan 2022 18:54:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:54:58: #1 finished! INFO @ Sat, 15 Jan 2022 18:54:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:54:58: #2 number of paired peaks: 368 WARNING @ Sat, 15 Jan 2022 18:54:58: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Sat, 15 Jan 2022 18:54:58: start model_add_line... INFO @ Sat, 15 Jan 2022 18:54:58: start X-correlation... INFO @ Sat, 15 Jan 2022 18:54:58: end of X-cor INFO @ Sat, 15 Jan 2022 18:54:58: #2 finished! INFO @ Sat, 15 Jan 2022 18:54:58: #2 predicted fragment length is 1 bps INFO @ Sat, 15 Jan 2022 18:54:58: #2 alternative fragment length(s) may be 1,23,60,84,101,116,130,147,174,188,197,211,218,223,297,338,363 bps INFO @ Sat, 15 Jan 2022 18:54:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.05_model.r WARNING @ Sat, 15 Jan 2022 18:54:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:54:58: #2 You may need to consider one of the other alternative d(s): 1,23,60,84,101,116,130,147,174,188,197,211,218,223,297,338,363 WARNING @ Sat, 15 Jan 2022 18:54:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:54:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:54:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:55:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:55:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:55:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:55:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.05_summits.bed INFO @ Sat, 15 Jan 2022 18:55:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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 @ Sat, 15 Jan 2022 18:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 15 Jan 2022 18:55:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:55:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:55:17: 1000000 INFO @ Sat, 15 Jan 2022 18:55:26: 2000000 INFO @ Sat, 15 Jan 2022 18:55:28: #1 tag size is determined as 101 bps INFO @ Sat, 15 Jan 2022 18:55:28: #1 tag size = 101 INFO @ Sat, 15 Jan 2022 18:55:28: #1 total tags in treatment: 2325594 INFO @ Sat, 15 Jan 2022 18:55:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:55:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:55:28: #1 tags after filtering in treatment: 2325594 INFO @ Sat, 15 Jan 2022 18:55:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:55:28: #1 finished! INFO @ Sat, 15 Jan 2022 18:55:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:55:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:55:29: #2 number of paired peaks: 368 WARNING @ Sat, 15 Jan 2022 18:55:29: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Sat, 15 Jan 2022 18:55:29: start model_add_line... INFO @ Sat, 15 Jan 2022 18:55:29: start X-correlation... INFO @ Sat, 15 Jan 2022 18:55:29: end of X-cor INFO @ Sat, 15 Jan 2022 18:55:29: #2 finished! INFO @ Sat, 15 Jan 2022 18:55:29: #2 predicted fragment length is 1 bps INFO @ Sat, 15 Jan 2022 18:55:29: #2 alternative fragment length(s) may be 1,23,60,84,101,116,130,147,174,188,197,211,218,223,297,338,363 bps INFO @ Sat, 15 Jan 2022 18:55:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.10_model.r WARNING @ Sat, 15 Jan 2022 18:55:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:55:29: #2 You may need to consider one of the other alternative d(s): 1,23,60,84,101,116,130,147,174,188,197,211,218,223,297,338,363 WARNING @ Sat, 15 Jan 2022 18:55:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:55:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:55:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:55:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:55:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:55:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:55:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.10_summits.bed INFO @ Sat, 15 Jan 2022 18:55:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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 @ Sat, 15 Jan 2022 18:55:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 15 Jan 2022 18:55:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:55:38: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:55:47: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:55:56: 2000000 INFO @ Sat, 15 Jan 2022 18:55:59: #1 tag size is determined as 101 bps INFO @ Sat, 15 Jan 2022 18:55:59: #1 tag size = 101 INFO @ Sat, 15 Jan 2022 18:55:59: #1 total tags in treatment: 2325594 INFO @ Sat, 15 Jan 2022 18:55:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:55:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:55:59: #1 tags after filtering in treatment: 2325594 INFO @ Sat, 15 Jan 2022 18:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:55:59: #1 finished! INFO @ Sat, 15 Jan 2022 18:55:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:55:59: #2 number of paired peaks: 368 WARNING @ Sat, 15 Jan 2022 18:55:59: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Sat, 15 Jan 2022 18:55:59: start model_add_line... INFO @ Sat, 15 Jan 2022 18:55:59: start X-correlation... INFO @ Sat, 15 Jan 2022 18:55:59: end of X-cor INFO @ Sat, 15 Jan 2022 18:55:59: #2 finished! INFO @ Sat, 15 Jan 2022 18:55:59: #2 predicted fragment length is 1 bps INFO @ Sat, 15 Jan 2022 18:55:59: #2 alternative fragment length(s) may be 1,23,60,84,101,116,130,147,174,188,197,211,218,223,297,338,363 bps INFO @ Sat, 15 Jan 2022 18:55:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.20_model.r WARNING @ Sat, 15 Jan 2022 18:55:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:55:59: #2 You may need to consider one of the other alternative d(s): 1,23,60,84,101,116,130,147,174,188,197,211,218,223,297,338,363 WARNING @ Sat, 15 Jan 2022 18:55:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:55:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:56:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:56:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:56:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:56:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8421789/SRX8421789.20_summits.bed INFO @ Sat, 15 Jan 2022 18:56:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling