Job ID = 14521262 SRX = SRX8245391 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10606518 spots for SRR11684602/SRR11684602.sra Written 10606518 spots for SRR11684602/SRR11684602.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: 00:07:37 10606518 reads; of these: 10606518 (100.00%) were paired; of these: 5636489 (53.14%) aligned concordantly 0 times 4545763 (42.86%) aligned concordantly exactly 1 time 424266 (4.00%) aligned concordantly >1 times ---- 5636489 pairs aligned concordantly 0 times; of these: 81545 (1.45%) aligned discordantly 1 time ---- 5554944 pairs aligned 0 times concordantly or discordantly; of these: 11109888 mates make up the pairs; of these: 6860568 (61.75%) aligned 0 times 3791163 (34.12%) aligned exactly 1 time 458157 (4.12%) aligned >1 times 67.66% overall alignment rate Time searching: 00:07:37 Overall time: 00:07:37 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] 516685 / 5045335 = 0.1024 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 21:01:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.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 21:01:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:09: 1000000 INFO @ Sat, 15 Jan 2022 21:01:16: 2000000 INFO @ Sat, 15 Jan 2022 21:01:22: 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 21:01:29: 4000000 INFO @ Sat, 15 Jan 2022 21:01:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.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 21:01:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:36: 5000000 INFO @ Sat, 15 Jan 2022 21:01:40: 1000000 INFO @ Sat, 15 Jan 2022 21:01:43: 6000000 INFO @ Sat, 15 Jan 2022 21:01:48: 2000000 INFO @ Sat, 15 Jan 2022 21:01:50: 7000000 INFO @ Sat, 15 Jan 2022 21:01:56: 3000000 INFO @ Sat, 15 Jan 2022 21:01:57: 8000000 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 21:02:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.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 21:02:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:02:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:02:04: 4000000 INFO @ Sat, 15 Jan 2022 21:02:04: 9000000 INFO @ Sat, 15 Jan 2022 21:02:10: 1000000 INFO @ Sat, 15 Jan 2022 21:02:12: 10000000 INFO @ Sat, 15 Jan 2022 21:02:12: 5000000 INFO @ Sat, 15 Jan 2022 21:02:18: 2000000 INFO @ Sat, 15 Jan 2022 21:02:19: 11000000 INFO @ Sat, 15 Jan 2022 21:02:20: 6000000 INFO @ Sat, 15 Jan 2022 21:02:26: 12000000 INFO @ Sat, 15 Jan 2022 21:02:27: 3000000 INFO @ Sat, 15 Jan 2022 21:02:28: 7000000 INFO @ Sat, 15 Jan 2022 21:02:34: 13000000 INFO @ Sat, 15 Jan 2022 21:02:35: 4000000 INFO @ Sat, 15 Jan 2022 21:02:36: 8000000 INFO @ Sat, 15 Jan 2022 21:02:36: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:02:36: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:02:36: #1 total tags in treatment: 4512956 INFO @ Sat, 15 Jan 2022 21:02:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:02:36: #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 21:02:36: #1 tags after filtering in treatment: 2136419 INFO @ Sat, 15 Jan 2022 21:02:36: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 15 Jan 2022 21:02:36: #1 finished! INFO @ Sat, 15 Jan 2022 21:02:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:02:36: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 21:02:36: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 21:02:36: start model_add_line... INFO @ Sat, 15 Jan 2022 21:02:36: start X-correlation... INFO @ Sat, 15 Jan 2022 21:02:37: end of X-cor INFO @ Sat, 15 Jan 2022 21:02:37: #2 finished! INFO @ Sat, 15 Jan 2022 21:02:37: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 21:02:37: #2 alternative fragment length(s) may be 13,53,92,124,195,236,252,308,344,390,421,458,479,492,528,579 bps INFO @ Sat, 15 Jan 2022 21:02:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.05_model.r WARNING @ Sat, 15 Jan 2022 21:02:37: #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 21:02:37: #2 You may need to consider one of the other alternative d(s): 13,53,92,124,195,236,252,308,344,390,421,458,479,492,528,579 WARNING @ Sat, 15 Jan 2022 21:02:37: #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 21:02:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:02:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:02:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:02:43: 5000000 INFO @ Sat, 15 Jan 2022 21:02:44: 9000000 INFO @ Sat, 15 Jan 2022 21:02:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:02:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:02:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.05_summits.bed INFO @ Sat, 15 Jan 2022 21:02:44: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:02:51: 6000000 INFO @ Sat, 15 Jan 2022 21:02:52: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:02:59: 7000000 INFO @ Sat, 15 Jan 2022 21:03:00: 11000000 INFO @ Sat, 15 Jan 2022 21:03:08: 8000000 INFO @ Sat, 15 Jan 2022 21:03:08: 12000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:03:16: 13000000 INFO @ Sat, 15 Jan 2022 21:03:16: 9000000 INFO @ Sat, 15 Jan 2022 21:03:19: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:03:19: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:03:19: #1 total tags in treatment: 4512956 INFO @ Sat, 15 Jan 2022 21:03:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:03:19: #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 21:03:19: #1 tags after filtering in treatment: 2136419 INFO @ Sat, 15 Jan 2022 21:03:19: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 15 Jan 2022 21:03:19: #1 finished! INFO @ Sat, 15 Jan 2022 21:03:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:03:19: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 21:03:19: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 21:03:19: start model_add_line... INFO @ Sat, 15 Jan 2022 21:03:19: start X-correlation... INFO @ Sat, 15 Jan 2022 21:03:19: end of X-cor INFO @ Sat, 15 Jan 2022 21:03:19: #2 finished! INFO @ Sat, 15 Jan 2022 21:03:19: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 21:03:19: #2 alternative fragment length(s) may be 13,53,92,124,195,236,252,308,344,390,421,458,479,492,528,579 bps INFO @ Sat, 15 Jan 2022 21:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.10_model.r WARNING @ Sat, 15 Jan 2022 21:03:19: #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 21:03:19: #2 You may need to consider one of the other alternative d(s): 13,53,92,124,195,236,252,308,344,390,421,458,479,492,528,579 WARNING @ Sat, 15 Jan 2022 21:03:19: #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 21:03:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:03:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:03:25: 10000000 INFO @ Sat, 15 Jan 2022 21:03:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:03:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:03:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.10_summits.bed INFO @ Sat, 15 Jan 2022 21:03:26: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:03:34: 11000000 INFO @ Sat, 15 Jan 2022 21:03:43: 12000000 INFO @ Sat, 15 Jan 2022 21:03:52: 13000000 INFO @ Sat, 15 Jan 2022 21:03:55: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:03:55: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:03:55: #1 total tags in treatment: 4512956 INFO @ Sat, 15 Jan 2022 21:03:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:03:55: #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 21:03:55: #1 tags after filtering in treatment: 2136419 INFO @ Sat, 15 Jan 2022 21:03:55: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 15 Jan 2022 21:03:55: #1 finished! INFO @ Sat, 15 Jan 2022 21:03:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:03:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:03:55: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 21:03:55: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 21:03:55: start model_add_line... INFO @ Sat, 15 Jan 2022 21:03:55: start X-correlation... INFO @ Sat, 15 Jan 2022 21:03:55: end of X-cor INFO @ Sat, 15 Jan 2022 21:03:55: #2 finished! INFO @ Sat, 15 Jan 2022 21:03:55: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 21:03:55: #2 alternative fragment length(s) may be 13,53,92,124,195,236,252,308,344,390,421,458,479,492,528,579 bps INFO @ Sat, 15 Jan 2022 21:03:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.20_model.r WARNING @ Sat, 15 Jan 2022 21:03:55: #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 21:03:55: #2 You may need to consider one of the other alternative d(s): 13,53,92,124,195,236,252,308,344,390,421,458,479,492,528,579 WARNING @ Sat, 15 Jan 2022 21:03:55: #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 21:03:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:03:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:04:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:04:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:04:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:04:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245391/SRX8245391.20_summits.bed INFO @ Sat, 15 Jan 2022 21:04:03: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling