Job ID = 14521267 SRX = SRX8245396 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10143255 spots for SRR11684607/SRR11684607.sra Written 10143255 spots for SRR11684607/SRR11684607.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: 00:06:16 10143255 reads; of these: 10143255 (100.00%) were paired; of these: 5563776 (54.85%) aligned concordantly 0 times 4007147 (39.51%) aligned concordantly exactly 1 time 572332 (5.64%) aligned concordantly >1 times ---- 5563776 pairs aligned concordantly 0 times; of these: 21064 (0.38%) aligned discordantly 1 time ---- 5542712 pairs aligned 0 times concordantly or discordantly; of these: 11085424 mates make up the pairs; of these: 6535440 (58.96%) aligned 0 times 3931326 (35.46%) aligned exactly 1 time 618658 (5.58%) aligned >1 times 67.78% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 236853 / 4599775 = 0.0515 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 20:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.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 20:56:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:56:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:56:22: 1000000 INFO @ Sat, 15 Jan 2022 20:56:26: 2000000 INFO @ Sat, 15 Jan 2022 20:56:31: 3000000 INFO @ Sat, 15 Jan 2022 20:56:36: 4000000 INFO @ Sat, 15 Jan 2022 20:56:40: 5000000 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 20:56:45: 6000000 INFO @ Sat, 15 Jan 2022 20:56:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.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 20:56:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:56:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:56:50: 7000000 INFO @ Sat, 15 Jan 2022 20:56:52: 1000000 INFO @ Sat, 15 Jan 2022 20:56:56: 8000000 INFO @ Sat, 15 Jan 2022 20:56:58: 2000000 INFO @ Sat, 15 Jan 2022 20:57:01: 9000000 INFO @ Sat, 15 Jan 2022 20:57:04: 3000000 INFO @ Sat, 15 Jan 2022 20:57:07: 10000000 INFO @ Sat, 15 Jan 2022 20:57:09: 4000000 INFO @ Sat, 15 Jan 2022 20:57:12: 11000000 INFO @ Sat, 15 Jan 2022 20:57:15: 5000000 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 20:57:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.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 20:57:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:57:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:57:18: 12000000 INFO @ Sat, 15 Jan 2022 20:57:20: 6000000 INFO @ Sat, 15 Jan 2022 20:57:23: 1000000 INFO @ Sat, 15 Jan 2022 20:57:24: 13000000 INFO @ Sat, 15 Jan 2022 20:57:25: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:57:25: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:57:25: #1 total tags in treatment: 4343329 INFO @ Sat, 15 Jan 2022 20:57:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:25: #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 20:57:25: #1 tags after filtering in treatment: 2639087 INFO @ Sat, 15 Jan 2022 20:57:25: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:57:25: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:25: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 20:57:25: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 20:57:25: start model_add_line... INFO @ Sat, 15 Jan 2022 20:57:25: start X-correlation... INFO @ Sat, 15 Jan 2022 20:57:25: end of X-cor INFO @ Sat, 15 Jan 2022 20:57:25: #2 finished! INFO @ Sat, 15 Jan 2022 20:57:25: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 20:57:25: #2 alternative fragment length(s) may be 53,117,167,192,240,310,335,350,369,401,451,494,517,521,539,580 bps INFO @ Sat, 15 Jan 2022 20:57:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.05_model.r WARNING @ Sat, 15 Jan 2022 20:57:25: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:57:25: #2 You may need to consider one of the other alternative d(s): 53,117,167,192,240,310,335,350,369,401,451,494,517,521,539,580 WARNING @ Sat, 15 Jan 2022 20:57:25: #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 20:57:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:57:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:57:26: 7000000 INFO @ Sat, 15 Jan 2022 20:57:29: 2000000 INFO @ Sat, 15 Jan 2022 20:57:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:57:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:57:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:57:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.05_summits.bed INFO @ Sat, 15 Jan 2022 20:57:31: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:57:32: 8000000 INFO @ Sat, 15 Jan 2022 20:57:35: 3000000 INFO @ Sat, 15 Jan 2022 20:57:37: 9000000 INFO @ Sat, 15 Jan 2022 20:57:42: 4000000 INFO @ Sat, 15 Jan 2022 20:57:43: 10000000 INFO @ Sat, 15 Jan 2022 20:57:48: 5000000 INFO @ Sat, 15 Jan 2022 20:57:49: 11000000 INFO @ Sat, 15 Jan 2022 20:57:53: 6000000 INFO @ Sat, 15 Jan 2022 20:57:55: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:57:59: 7000000 INFO @ Sat, 15 Jan 2022 20:58:01: 13000000 INFO @ Sat, 15 Jan 2022 20:58:03: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:58:03: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:58:03: #1 total tags in treatment: 4343329 INFO @ Sat, 15 Jan 2022 20:58:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:58:03: #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 20:58:03: #1 tags after filtering in treatment: 2639087 INFO @ Sat, 15 Jan 2022 20:58:03: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:58:03: #1 finished! INFO @ Sat, 15 Jan 2022 20:58:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:58:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:58:03: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 20:58:03: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 20:58:03: start model_add_line... INFO @ Sat, 15 Jan 2022 20:58:03: start X-correlation... INFO @ Sat, 15 Jan 2022 20:58:03: end of X-cor INFO @ Sat, 15 Jan 2022 20:58:03: #2 finished! INFO @ Sat, 15 Jan 2022 20:58:03: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 20:58:03: #2 alternative fragment length(s) may be 53,117,167,192,240,310,335,350,369,401,451,494,517,521,539,580 bps INFO @ Sat, 15 Jan 2022 20:58:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.10_model.r WARNING @ Sat, 15 Jan 2022 20:58:03: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:58:03: #2 You may need to consider one of the other alternative d(s): 53,117,167,192,240,310,335,350,369,401,451,494,517,521,539,580 WARNING @ Sat, 15 Jan 2022 20:58:03: #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 20:58:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:58:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:58:06: 8000000 INFO @ Sat, 15 Jan 2022 20:58:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:58:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:58:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:58:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.10_summits.bed INFO @ Sat, 15 Jan 2022 20:58:09: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:58:12: 9000000 INFO @ Sat, 15 Jan 2022 20:58:18: 10000000 INFO @ Sat, 15 Jan 2022 20:58:24: 11000000 INFO @ Sat, 15 Jan 2022 20:58:30: 12000000 INFO @ Sat, 15 Jan 2022 20:58:35: 13000000 INFO @ Sat, 15 Jan 2022 20:58:37: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:58:37: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:58:37: #1 total tags in treatment: 4343329 INFO @ Sat, 15 Jan 2022 20:58:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:58:37: #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 20:58:37: #1 tags after filtering in treatment: 2639087 INFO @ Sat, 15 Jan 2022 20:58:37: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:58:37: #1 finished! INFO @ Sat, 15 Jan 2022 20:58:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:58:37: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 20:58:37: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 20:58:37: start model_add_line... INFO @ Sat, 15 Jan 2022 20:58:37: start X-correlation... INFO @ Sat, 15 Jan 2022 20:58:37: end of X-cor INFO @ Sat, 15 Jan 2022 20:58:37: #2 finished! INFO @ Sat, 15 Jan 2022 20:58:37: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 20:58:37: #2 alternative fragment length(s) may be 53,117,167,192,240,310,335,350,369,401,451,494,517,521,539,580 bps INFO @ Sat, 15 Jan 2022 20:58:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.20_model.r WARNING @ Sat, 15 Jan 2022 20:58:37: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:58:37: #2 You may need to consider one of the other alternative d(s): 53,117,167,192,240,310,335,350,369,401,451,494,517,521,539,580 WARNING @ Sat, 15 Jan 2022 20:58:37: #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 20:58:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:58:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:58:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:58:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:58:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245396/SRX8245396.20_summits.bed INFO @ Sat, 15 Jan 2022 20:58:43: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling