Job ID = 14521870 SRX = ERX4439561 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3468099 spots for ERR4501490/ERR4501490.sra Written 3468099 spots for ERR4501490/ERR4501490.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: 00:04:02 3468099 reads; of these: 3468099 (100.00%) were paired; of these: 847181 (24.43%) aligned concordantly 0 times 2329149 (67.16%) aligned concordantly exactly 1 time 291769 (8.41%) aligned concordantly >1 times ---- 847181 pairs aligned concordantly 0 times; of these: 406327 (47.96%) aligned discordantly 1 time ---- 440854 pairs aligned 0 times concordantly or discordantly; of these: 881708 mates make up the pairs; of these: 722162 (81.90%) aligned 0 times 56690 (6.43%) aligned exactly 1 time 102856 (11.67%) aligned >1 times 89.59% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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_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] 35750 / 2999951 = 0.0119 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 21:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.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 21:55:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:55:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:55:32: 1000000 INFO @ Sat, 15 Jan 2022 21:55:38: 2000000 INFO @ Sat, 15 Jan 2022 21:55:44: 3000000 INFO @ Sat, 15 Jan 2022 21:55:51: 4000000 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 21:55:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.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 21:55:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:55:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:55:57: 5000000 INFO @ Sat, 15 Jan 2022 21:56:02: 1000000 INFO @ Sat, 15 Jan 2022 21:56:04: 6000000 INFO @ Sat, 15 Jan 2022 21:56:05: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:56:05: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:56:05: #1 total tags in treatment: 2590971 INFO @ Sat, 15 Jan 2022 21:56:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:56:05: #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 21:56:05: #1 tags after filtering in treatment: 2340256 INFO @ Sat, 15 Jan 2022 21:56:05: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:56:05: #1 finished! INFO @ Sat, 15 Jan 2022 21:56:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:56:05: #2 number of paired peaks: 126 WARNING @ Sat, 15 Jan 2022 21:56:05: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 15 Jan 2022 21:56:05: start model_add_line... INFO @ Sat, 15 Jan 2022 21:56:05: start X-correlation... INFO @ Sat, 15 Jan 2022 21:56:05: end of X-cor INFO @ Sat, 15 Jan 2022 21:56:05: #2 finished! INFO @ Sat, 15 Jan 2022 21:56:05: #2 predicted fragment length is 157 bps INFO @ Sat, 15 Jan 2022 21:56:05: #2 alternative fragment length(s) may be 1,139,157,174,219 bps INFO @ Sat, 15 Jan 2022 21:56:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.05_model.r WARNING @ Sat, 15 Jan 2022 21:56:05: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:56:05: #2 You may need to consider one of the other alternative d(s): 1,139,157,174,219 WARNING @ Sat, 15 Jan 2022 21:56:05: #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 21:56:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:56:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:56:09: 2000000 INFO @ Sat, 15 Jan 2022 21:56:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:56:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:56:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:56:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.05_summits.bed INFO @ Sat, 15 Jan 2022 21:56:12: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (54 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:56:15: 3000000 INFO @ Sat, 15 Jan 2022 21:56:21: 4000000 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 21:56:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.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 21:56:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:56:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:56:28: 5000000 INFO @ Sat, 15 Jan 2022 21:56:33: 1000000 INFO @ Sat, 15 Jan 2022 21:56:35: 6000000 INFO @ Sat, 15 Jan 2022 21:56:36: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:56:36: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:56:36: #1 total tags in treatment: 2590971 INFO @ Sat, 15 Jan 2022 21:56:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:56:36: #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 21:56:36: #1 tags after filtering in treatment: 2340256 INFO @ Sat, 15 Jan 2022 21:56:36: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:56:36: #1 finished! INFO @ Sat, 15 Jan 2022 21:56:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:56:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:56:36: #2 number of paired peaks: 126 WARNING @ Sat, 15 Jan 2022 21:56:36: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 15 Jan 2022 21:56:36: start model_add_line... INFO @ Sat, 15 Jan 2022 21:56:36: start X-correlation... INFO @ Sat, 15 Jan 2022 21:56:36: end of X-cor INFO @ Sat, 15 Jan 2022 21:56:36: #2 finished! INFO @ Sat, 15 Jan 2022 21:56:36: #2 predicted fragment length is 157 bps INFO @ Sat, 15 Jan 2022 21:56:36: #2 alternative fragment length(s) may be 1,139,157,174,219 bps INFO @ Sat, 15 Jan 2022 21:56:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.10_model.r WARNING @ Sat, 15 Jan 2022 21:56:36: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:56:36: #2 You may need to consider one of the other alternative d(s): 1,139,157,174,219 WARNING @ Sat, 15 Jan 2022 21:56:36: #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 21:56:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:56:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:56:40: 2000000 INFO @ Sat, 15 Jan 2022 21:56:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:56:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:56:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:56:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.10_summits.bed INFO @ Sat, 15 Jan 2022 21:56:43: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:56:46: 3000000 INFO @ Sat, 15 Jan 2022 21:56:53: 4000000 INFO @ Sat, 15 Jan 2022 21:56:59: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:57:05: 6000000 INFO @ Sat, 15 Jan 2022 21:57:06: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:57:06: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:57:06: #1 total tags in treatment: 2590971 INFO @ Sat, 15 Jan 2022 21:57:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:57:06: #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 21:57:06: #1 tags after filtering in treatment: 2340256 INFO @ Sat, 15 Jan 2022 21:57:06: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:57:06: #1 finished! INFO @ Sat, 15 Jan 2022 21:57:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:57:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:57:06: #2 number of paired peaks: 126 WARNING @ Sat, 15 Jan 2022 21:57:06: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 15 Jan 2022 21:57:06: start model_add_line... INFO @ Sat, 15 Jan 2022 21:57:06: start X-correlation... INFO @ Sat, 15 Jan 2022 21:57:06: end of X-cor INFO @ Sat, 15 Jan 2022 21:57:06: #2 finished! INFO @ Sat, 15 Jan 2022 21:57:06: #2 predicted fragment length is 157 bps INFO @ Sat, 15 Jan 2022 21:57:06: #2 alternative fragment length(s) may be 1,139,157,174,219 bps INFO @ Sat, 15 Jan 2022 21:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.20_model.r WARNING @ Sat, 15 Jan 2022 21:57:06: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:57:06: #2 You may need to consider one of the other alternative d(s): 1,139,157,174,219 WARNING @ Sat, 15 Jan 2022 21:57:06: #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 21:57:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:57:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:57:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:57:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:57:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:57:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439561/ERX4439561.20_summits.bed INFO @ Sat, 15 Jan 2022 21:57:13: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling