Job ID = 7108598 SRX = SRX7960946 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6555085 spots for SRR11359451/SRR11359451.sra Written 6555085 spots for SRR11359451/SRR11359451.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: 00:02:21 6555085 reads; of these: 6555085 (100.00%) were unpaired; of these: 1675488 (25.56%) aligned 0 times 3249840 (49.58%) aligned exactly 1 time 1629757 (24.86%) aligned >1 times 74.44% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 2550762 / 4879597 = 0.5227 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.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 @ Wed, 22 Jul 2020 13:43:58: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:43:58: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:44:09: 1000000 INFO @ Wed, 22 Jul 2020 13:44:20: 2000000 INFO @ Wed, 22 Jul 2020 13:44:23: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:44:23: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:44:23: #1 total tags in treatment: 2328835 INFO @ Wed, 22 Jul 2020 13:44:23: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:44:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:44:23: #1 tags after filtering in treatment: 2328835 INFO @ Wed, 22 Jul 2020 13:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:44:23: #1 finished! INFO @ Wed, 22 Jul 2020 13:44:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:44:23: #2 number of paired peaks: 169 WARNING @ Wed, 22 Jul 2020 13:44:23: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Wed, 22 Jul 2020 13:44:23: start model_add_line... INFO @ Wed, 22 Jul 2020 13:44:23: start X-correlation... INFO @ Wed, 22 Jul 2020 13:44:23: end of X-cor INFO @ Wed, 22 Jul 2020 13:44:23: #2 finished! INFO @ Wed, 22 Jul 2020 13:44:23: #2 predicted fragment length is 240 bps INFO @ Wed, 22 Jul 2020 13:44:23: #2 alternative fragment length(s) may be 3,223,240,262 bps INFO @ Wed, 22 Jul 2020 13:44:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.05_model.r WARNING @ Wed, 22 Jul 2020 13:44:23: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:44:23: #2 You may need to consider one of the other alternative d(s): 3,223,240,262 WARNING @ Wed, 22 Jul 2020 13:44:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:44:23: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:44:23: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.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 @ Wed, 22 Jul 2020 13:44:28: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:44:28: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:44:31: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.05_summits.bed INFO @ Wed, 22 Jul 2020 13:44:33: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (451 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:44:40: 1000000 INFO @ Wed, 22 Jul 2020 13:44:51: 2000000 INFO @ Wed, 22 Jul 2020 13:44:54: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:44:54: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:44:54: #1 total tags in treatment: 2328835 INFO @ Wed, 22 Jul 2020 13:44:54: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:44:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:44:54: #1 tags after filtering in treatment: 2328835 INFO @ Wed, 22 Jul 2020 13:44:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:44:54: #1 finished! INFO @ Wed, 22 Jul 2020 13:44:54: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:44:54: #2 number of paired peaks: 169 WARNING @ Wed, 22 Jul 2020 13:44:54: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Wed, 22 Jul 2020 13:44:54: start model_add_line... INFO @ Wed, 22 Jul 2020 13:44:54: start X-correlation... INFO @ Wed, 22 Jul 2020 13:44:54: end of X-cor INFO @ Wed, 22 Jul 2020 13:44:54: #2 finished! INFO @ Wed, 22 Jul 2020 13:44:54: #2 predicted fragment length is 240 bps INFO @ Wed, 22 Jul 2020 13:44:54: #2 alternative fragment length(s) may be 3,223,240,262 bps INFO @ Wed, 22 Jul 2020 13:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.10_model.r WARNING @ Wed, 22 Jul 2020 13:44:54: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:44:54: #2 You may need to consider one of the other alternative d(s): 3,223,240,262 WARNING @ Wed, 22 Jul 2020 13:44:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:44:54: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:44:54: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:44:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.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 @ Wed, 22 Jul 2020 13:44:58: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:44:58: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:45:02: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:45:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:45:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:45:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.10_summits.bed INFO @ Wed, 22 Jul 2020 13:45:04: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:45:09: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:45:20: 2000000 INFO @ Wed, 22 Jul 2020 13:45:23: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:45:23: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:45:23: #1 total tags in treatment: 2328835 INFO @ Wed, 22 Jul 2020 13:45:23: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:45:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:45:23: #1 tags after filtering in treatment: 2328835 INFO @ Wed, 22 Jul 2020 13:45:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:45:23: #1 finished! INFO @ Wed, 22 Jul 2020 13:45:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:45:24: #2 number of paired peaks: 169 WARNING @ Wed, 22 Jul 2020 13:45:24: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Wed, 22 Jul 2020 13:45:24: start model_add_line... INFO @ Wed, 22 Jul 2020 13:45:24: start X-correlation... INFO @ Wed, 22 Jul 2020 13:45:24: end of X-cor INFO @ Wed, 22 Jul 2020 13:45:24: #2 finished! INFO @ Wed, 22 Jul 2020 13:45:24: #2 predicted fragment length is 240 bps INFO @ Wed, 22 Jul 2020 13:45:24: #2 alternative fragment length(s) may be 3,223,240,262 bps INFO @ Wed, 22 Jul 2020 13:45:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.20_model.r WARNING @ Wed, 22 Jul 2020 13:45:24: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:45:24: #2 You may need to consider one of the other alternative d(s): 3,223,240,262 WARNING @ Wed, 22 Jul 2020 13:45:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:45:24: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:45:31: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:45:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:45:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:45:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960946/SRX7960946.20_summits.bed INFO @ Wed, 22 Jul 2020 13:45:33: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (75 records, 4 fields): 1 millis CompletedMACS2peakCalling