Job ID = 14521474 SRX = SRX8833544 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16955813 spots for SRR12333580/SRR12333580.sra Written 16955813 spots for SRR12333580/SRR12333580.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: 00:02:10 16955813 reads; of these: 16955813 (100.00%) were unpaired; of these: 3966731 (23.39%) aligned 0 times 11536138 (68.04%) aligned exactly 1 time 1452944 (8.57%) aligned >1 times 76.61% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9517116 / 12989082 = 0.7327 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 21:07:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.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 21:07:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:07:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:07:35: 1000000 INFO @ Sat, 15 Jan 2022 21:07:40: 2000000 INFO @ Sat, 15 Jan 2022 21:07:46: 3000000 INFO @ Sat, 15 Jan 2022 21:07:48: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:07:48: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:07:48: #1 total tags in treatment: 3471966 INFO @ Sat, 15 Jan 2022 21:07:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:07:48: #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 21:07:48: #1 tags after filtering in treatment: 3471966 INFO @ Sat, 15 Jan 2022 21:07:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 21:07:48: #1 finished! INFO @ Sat, 15 Jan 2022 21:07:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:07:48: #2 number of paired peaks: 206 WARNING @ Sat, 15 Jan 2022 21:07:48: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 15 Jan 2022 21:07:48: start model_add_line... INFO @ Sat, 15 Jan 2022 21:07:49: start X-correlation... INFO @ Sat, 15 Jan 2022 21:07:49: end of X-cor INFO @ Sat, 15 Jan 2022 21:07:49: #2 finished! INFO @ Sat, 15 Jan 2022 21:07:49: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 21:07:49: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sat, 15 Jan 2022 21:07:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.05_model.r WARNING @ Sat, 15 Jan 2022 21:07:49: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:07:49: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sat, 15 Jan 2022 21:07:49: #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 21:07:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:07:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:07:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:07:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:07:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:07:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.05_summits.bed INFO @ Sat, 15 Jan 2022 21:07:57: Done! 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 pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1434 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.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 21:07:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:07:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:08:05: 1000000 INFO @ Sat, 15 Jan 2022 21:08:11: 2000000 INFO @ Sat, 15 Jan 2022 21:08:18: 3000000 INFO @ Sat, 15 Jan 2022 21:08:20: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:08:20: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:08:20: #1 total tags in treatment: 3471966 INFO @ Sat, 15 Jan 2022 21:08:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:08:20: #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 21:08:20: #1 tags after filtering in treatment: 3471966 INFO @ Sat, 15 Jan 2022 21:08:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 21:08:20: #1 finished! INFO @ Sat, 15 Jan 2022 21:08:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:08:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:08:21: #2 number of paired peaks: 206 WARNING @ Sat, 15 Jan 2022 21:08:21: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 15 Jan 2022 21:08:21: start model_add_line... INFO @ Sat, 15 Jan 2022 21:08:21: start X-correlation... INFO @ Sat, 15 Jan 2022 21:08:21: end of X-cor INFO @ Sat, 15 Jan 2022 21:08:21: #2 finished! INFO @ Sat, 15 Jan 2022 21:08:21: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 21:08:21: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sat, 15 Jan 2022 21:08:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.10_model.r WARNING @ Sat, 15 Jan 2022 21:08:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:08:21: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sat, 15 Jan 2022 21:08:21: #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 21:08:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:08:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:08:27: #3 Call peaks for each chromosome... 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 21:08:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.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 21:08:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:08:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:08:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:08:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:08:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.10_summits.bed INFO @ Sat, 15 Jan 2022 21:08:29: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (707 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:08:35: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:08:41: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:08:47: 3000000 INFO @ Sat, 15 Jan 2022 21:08:50: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:08:50: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:08:50: #1 total tags in treatment: 3471966 INFO @ Sat, 15 Jan 2022 21:08:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:08:50: #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 21:08:50: #1 tags after filtering in treatment: 3471966 INFO @ Sat, 15 Jan 2022 21:08:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 21:08:50: #1 finished! INFO @ Sat, 15 Jan 2022 21:08:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:08:50: #2 number of paired peaks: 206 WARNING @ Sat, 15 Jan 2022 21:08:50: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 15 Jan 2022 21:08:50: start model_add_line... INFO @ Sat, 15 Jan 2022 21:08:50: start X-correlation... INFO @ Sat, 15 Jan 2022 21:08:50: end of X-cor INFO @ Sat, 15 Jan 2022 21:08:50: #2 finished! INFO @ Sat, 15 Jan 2022 21:08:50: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 21:08:50: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sat, 15 Jan 2022 21:08:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.20_model.r WARNING @ Sat, 15 Jan 2022 21:08:50: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:08:50: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sat, 15 Jan 2022 21:08:50: #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 21:08:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:08:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:08:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:08:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8833544/SRX8833544.20_summits.bed INFO @ Sat, 15 Jan 2022 21:08:59: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 1 millis CompletedMACS2peakCalling