Job ID = 14521965 SRX = SRX6950509 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3519201 spots for SRR10231169/SRR10231169.sra Written 3519201 spots for SRR10231169/SRR10231169.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: 00:05:57 3519201 reads; of these: 3519201 (100.00%) were paired; of these: 757281 (21.52%) aligned concordantly 0 times 2513515 (71.42%) aligned concordantly exactly 1 time 248405 (7.06%) aligned concordantly >1 times ---- 757281 pairs aligned concordantly 0 times; of these: 292216 (38.59%) aligned discordantly 1 time ---- 465065 pairs aligned 0 times concordantly or discordantly; of these: 930130 mates make up the pairs; of these: 835318 (89.81%) aligned 0 times 31995 (3.44%) aligned exactly 1 time 62817 (6.75%) aligned >1 times 88.13% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 619112 / 2471347 = 0.2505 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 22:04:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.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 22:04:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:04:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:04:45: 1000000 INFO @ Sat, 15 Jan 2022 22:04:54: 2000000 INFO @ Sat, 15 Jan 2022 22:05:03: 3000000 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 22:05:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.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 22:05:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:05:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:05:12: 4000000 INFO @ Sat, 15 Jan 2022 22:05:16: 1000000 INFO @ Sat, 15 Jan 2022 22:05:21: #1 tag size is determined as 107 bps INFO @ Sat, 15 Jan 2022 22:05:21: #1 tag size = 107 INFO @ Sat, 15 Jan 2022 22:05:21: #1 total tags in treatment: 2212653 INFO @ Sat, 15 Jan 2022 22:05:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:05:21: #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 22:05:21: #1 tags after filtering in treatment: 1796377 INFO @ Sat, 15 Jan 2022 22:05:21: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 22:05:21: #1 finished! INFO @ Sat, 15 Jan 2022 22:05:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:05:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:05:22: #2 number of paired peaks: 211 WARNING @ Sat, 15 Jan 2022 22:05:22: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sat, 15 Jan 2022 22:05:22: start model_add_line... INFO @ Sat, 15 Jan 2022 22:05:22: start X-correlation... INFO @ Sat, 15 Jan 2022 22:05:22: end of X-cor INFO @ Sat, 15 Jan 2022 22:05:22: #2 finished! INFO @ Sat, 15 Jan 2022 22:05:22: #2 predicted fragment length is 108 bps INFO @ Sat, 15 Jan 2022 22:05:22: #2 alternative fragment length(s) may be 3,108,118 bps INFO @ Sat, 15 Jan 2022 22:05:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.05_model.r WARNING @ Sat, 15 Jan 2022 22:05:22: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:05:22: #2 You may need to consider one of the other alternative d(s): 3,108,118 WARNING @ Sat, 15 Jan 2022 22:05:22: #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 22:05:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:05:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:05:25: 2000000 INFO @ Sat, 15 Jan 2022 22:05:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:05:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:05:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:05:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.05_summits.bed INFO @ Sat, 15 Jan 2022 22:05:28: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (665 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 22:05:34: 3000000 INFO @ Sat, 15 Jan 2022 22:05:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.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 22:05:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:05:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:05:43: 4000000 INFO @ Sat, 15 Jan 2022 22:05:48: 1000000 INFO @ Sat, 15 Jan 2022 22:05:53: #1 tag size is determined as 107 bps INFO @ Sat, 15 Jan 2022 22:05:53: #1 tag size = 107 INFO @ Sat, 15 Jan 2022 22:05:53: #1 total tags in treatment: 2212653 INFO @ Sat, 15 Jan 2022 22:05:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:05:53: #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 22:05:53: #1 tags after filtering in treatment: 1796377 INFO @ Sat, 15 Jan 2022 22:05:53: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 22:05:53: #1 finished! INFO @ Sat, 15 Jan 2022 22:05:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:05:53: #2 number of paired peaks: 211 WARNING @ Sat, 15 Jan 2022 22:05:53: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sat, 15 Jan 2022 22:05:53: start model_add_line... INFO @ Sat, 15 Jan 2022 22:05:53: start X-correlation... INFO @ Sat, 15 Jan 2022 22:05:53: end of X-cor INFO @ Sat, 15 Jan 2022 22:05:53: #2 finished! INFO @ Sat, 15 Jan 2022 22:05:53: #2 predicted fragment length is 108 bps INFO @ Sat, 15 Jan 2022 22:05:53: #2 alternative fragment length(s) may be 3,108,118 bps INFO @ Sat, 15 Jan 2022 22:05:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.10_model.r WARNING @ Sat, 15 Jan 2022 22:05:53: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:05:53: #2 You may need to consider one of the other alternative d(s): 3,108,118 WARNING @ Sat, 15 Jan 2022 22:05:53: #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 22:05:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:05:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:05:59: 2000000 INFO @ Sat, 15 Jan 2022 22:06:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:06:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:06:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.10_summits.bed INFO @ Sat, 15 Jan 2022 22:06:00: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:06:10: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:06:21: 4000000 INFO @ Sat, 15 Jan 2022 22:06:31: #1 tag size is determined as 107 bps INFO @ Sat, 15 Jan 2022 22:06:31: #1 tag size = 107 INFO @ Sat, 15 Jan 2022 22:06:31: #1 total tags in treatment: 2212653 INFO @ Sat, 15 Jan 2022 22:06:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:06:31: #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 22:06:31: #1 tags after filtering in treatment: 1796377 INFO @ Sat, 15 Jan 2022 22:06:31: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 22:06:31: #1 finished! INFO @ Sat, 15 Jan 2022 22:06:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:06:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:06:31: #2 number of paired peaks: 211 WARNING @ Sat, 15 Jan 2022 22:06:31: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sat, 15 Jan 2022 22:06:31: start model_add_line... INFO @ Sat, 15 Jan 2022 22:06:31: start X-correlation... INFO @ Sat, 15 Jan 2022 22:06:31: end of X-cor INFO @ Sat, 15 Jan 2022 22:06:31: #2 finished! INFO @ Sat, 15 Jan 2022 22:06:31: #2 predicted fragment length is 108 bps INFO @ Sat, 15 Jan 2022 22:06:31: #2 alternative fragment length(s) may be 3,108,118 bps INFO @ Sat, 15 Jan 2022 22:06:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.20_model.r WARNING @ Sat, 15 Jan 2022 22:06:31: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:06:31: #2 You may need to consider one of the other alternative d(s): 3,108,118 WARNING @ Sat, 15 Jan 2022 22:06:31: #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 22:06:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:06:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:06:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:06:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:06:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:06:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950509/SRX6950509.20_summits.bed INFO @ Sat, 15 Jan 2022 22:06:38: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (170 records, 4 fields): 3 millis CompletedMACS2peakCalling