Job ID = 14521326 SRX = SRX9278492 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 2048583 spots for SRR12809890/SRR12809890.sra Written 2048583 spots for SRR12809890/SRR12809890.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: 00:00:58 2048583 reads; of these: 2048583 (100.00%) were unpaired; of these: 46011 (2.25%) aligned 0 times 1828212 (89.24%) aligned exactly 1 time 174360 (8.51%) aligned >1 times 97.75% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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] 221982 / 2002572 = 0.1108 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 20:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.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 20:52:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:52:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:52:45: 1000000 INFO @ Sat, 15 Jan 2022 20:52:51: #1 tag size is determined as 143 bps INFO @ Sat, 15 Jan 2022 20:52:51: #1 tag size = 143 INFO @ Sat, 15 Jan 2022 20:52:51: #1 total tags in treatment: 1780590 INFO @ Sat, 15 Jan 2022 20:52:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:51: #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 20:52:51: #1 tags after filtering in treatment: 1780590 INFO @ Sat, 15 Jan 2022 20:52:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:52:51: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:51: #2 number of paired peaks: 202 WARNING @ Sat, 15 Jan 2022 20:52:51: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:51: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:51: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:51: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:51: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:51: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 20:52:51: #2 alternative fragment length(s) may be 4,117,133,141,145,172 bps INFO @ Sat, 15 Jan 2022 20:52:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.05_model.r WARNING @ Sat, 15 Jan 2022 20:52:51: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:52:51: #2 You may need to consider one of the other alternative d(s): 4,117,133,141,145,172 WARNING @ Sat, 15 Jan 2022 20:52:51: #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 20:52:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.05_summits.bed INFO @ Sat, 15 Jan 2022 20:52:59: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (781 records, 4 fields): 4 millis 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 20:53:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.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 20:53:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:53:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:53:15: 1000000 INFO @ Sat, 15 Jan 2022 20:53:21: #1 tag size is determined as 143 bps INFO @ Sat, 15 Jan 2022 20:53:21: #1 tag size = 143 INFO @ Sat, 15 Jan 2022 20:53:21: #1 total tags in treatment: 1780590 INFO @ Sat, 15 Jan 2022 20:53:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:53:21: #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 20:53:21: #1 tags after filtering in treatment: 1780590 INFO @ Sat, 15 Jan 2022 20:53:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:53:21: #1 finished! INFO @ Sat, 15 Jan 2022 20:53:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:53:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:53:21: #2 number of paired peaks: 202 WARNING @ Sat, 15 Jan 2022 20:53:21: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sat, 15 Jan 2022 20:53:21: start model_add_line... INFO @ Sat, 15 Jan 2022 20:53:21: start X-correlation... INFO @ Sat, 15 Jan 2022 20:53:21: end of X-cor INFO @ Sat, 15 Jan 2022 20:53:21: #2 finished! INFO @ Sat, 15 Jan 2022 20:53:21: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 20:53:21: #2 alternative fragment length(s) may be 4,117,133,141,145,172 bps INFO @ Sat, 15 Jan 2022 20:53:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.10_model.r WARNING @ Sat, 15 Jan 2022 20:53:21: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:53:21: #2 You may need to consider one of the other alternative d(s): 4,117,133,141,145,172 WARNING @ Sat, 15 Jan 2022 20:53:21: #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 20:53:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:53:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:53:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.10_summits.bed INFO @ Sat, 15 Jan 2022 20:53:29: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (486 records, 4 fields): 3 millis 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 20:53:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.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 20:53:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:53:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:53:44: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:53:50: #1 tag size is determined as 143 bps INFO @ Sat, 15 Jan 2022 20:53:50: #1 tag size = 143 INFO @ Sat, 15 Jan 2022 20:53:50: #1 total tags in treatment: 1780590 INFO @ Sat, 15 Jan 2022 20:53:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:53:50: #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 20:53:51: #1 tags after filtering in treatment: 1780590 INFO @ Sat, 15 Jan 2022 20:53:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:53:51: #1 finished! INFO @ Sat, 15 Jan 2022 20:53:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:53:51: #2 number of paired peaks: 202 WARNING @ Sat, 15 Jan 2022 20:53:51: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sat, 15 Jan 2022 20:53:51: start model_add_line... INFO @ Sat, 15 Jan 2022 20:53:51: start X-correlation... INFO @ Sat, 15 Jan 2022 20:53:51: end of X-cor INFO @ Sat, 15 Jan 2022 20:53:51: #2 finished! INFO @ Sat, 15 Jan 2022 20:53:51: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 20:53:51: #2 alternative fragment length(s) may be 4,117,133,141,145,172 bps INFO @ Sat, 15 Jan 2022 20:53:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.20_model.r WARNING @ Sat, 15 Jan 2022 20:53:51: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:53:51: #2 You may need to consider one of the other alternative d(s): 4,117,133,141,145,172 WARNING @ Sat, 15 Jan 2022 20:53:51: #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 20:53:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:53:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:53:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:53:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:53:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:53:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9278492/SRX9278492.20_summits.bed INFO @ Sat, 15 Jan 2022 20:53:58: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 2 millis CompletedMACS2peakCalling