Job ID = 14520782 SRX = SRX8245400 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9029341 spots for SRR11684611/SRR11684611.sra Written 9029341 spots for SRR11684611/SRR11684611.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: 00:04:09 9029341 reads; of these: 9029341 (100.00%) were paired; of these: 5213817 (57.74%) aligned concordantly 0 times 3502255 (38.79%) aligned concordantly exactly 1 time 313269 (3.47%) aligned concordantly >1 times ---- 5213817 pairs aligned concordantly 0 times; of these: 16807 (0.32%) aligned discordantly 1 time ---- 5197010 pairs aligned 0 times concordantly or discordantly; of these: 10394020 mates make up the pairs; of these: 6573337 (63.24%) aligned 0 times 3411662 (32.82%) aligned exactly 1 time 409021 (3.94%) aligned >1 times 63.60% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 281445 / 3829763 = 0.0735 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 20:03:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.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 20:03:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:03:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:03:24: 1000000 INFO @ Sat, 15 Jan 2022 20:03:28: 2000000 INFO @ Sat, 15 Jan 2022 20:03:32: 3000000 INFO @ Sat, 15 Jan 2022 20:03:36: 4000000 INFO @ Sat, 15 Jan 2022 20:03:39: 5000000 INFO @ Sat, 15 Jan 2022 20:03:43: 6000000 INFO @ Sat, 15 Jan 2022 20:03:47: 7000000 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 20:03:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.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 20:03:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:03:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:03:52: 8000000 INFO @ Sat, 15 Jan 2022 20:03:54: 1000000 INFO @ Sat, 15 Jan 2022 20:03:56: 9000000 INFO @ Sat, 15 Jan 2022 20:03:58: 2000000 INFO @ Sat, 15 Jan 2022 20:04:00: 10000000 INFO @ Sat, 15 Jan 2022 20:04:02: 3000000 INFO @ Sat, 15 Jan 2022 20:04:04: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:04:04: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:04:04: #1 total tags in treatment: 3535830 INFO @ Sat, 15 Jan 2022 20:04:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:04:04: #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 20:04:04: #1 tags after filtering in treatment: 1824870 INFO @ Sat, 15 Jan 2022 20:04:04: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 15 Jan 2022 20:04:04: #1 finished! INFO @ Sat, 15 Jan 2022 20:04:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:04:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:04:04: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:04:04: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:04:04: start model_add_line... INFO @ Sat, 15 Jan 2022 20:04:04: start X-correlation... INFO @ Sat, 15 Jan 2022 20:04:04: end of X-cor INFO @ Sat, 15 Jan 2022 20:04:04: #2 finished! INFO @ Sat, 15 Jan 2022 20:04:04: #2 predicted fragment length is 61 bps INFO @ Sat, 15 Jan 2022 20:04:04: #2 alternative fragment length(s) may be 27,61,132,186,220,243,265,288,309,354,357,397,424,430,480,486,509,531,547,565 bps INFO @ Sat, 15 Jan 2022 20:04:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.05_model.r WARNING @ Sat, 15 Jan 2022 20:04:04: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:04:04: #2 You may need to consider one of the other alternative d(s): 27,61,132,186,220,243,265,288,309,354,357,397,424,430,480,486,509,531,547,565 WARNING @ Sat, 15 Jan 2022 20:04:04: #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 20:04:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:04:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:04:06: 4000000 INFO @ Sat, 15 Jan 2022 20:04:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:04:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:04:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.05_summits.bed INFO @ Sat, 15 Jan 2022 20:04:09: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (137 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:04:10: 5000000 INFO @ Sat, 15 Jan 2022 20:04:14: 6000000 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 20:04:18: 7000000 INFO @ Sat, 15 Jan 2022 20:04:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.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 20:04:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:04:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:04:22: 8000000 INFO @ Sat, 15 Jan 2022 20:04:24: 1000000 INFO @ Sat, 15 Jan 2022 20:04:26: 9000000 INFO @ Sat, 15 Jan 2022 20:04:28: 2000000 INFO @ Sat, 15 Jan 2022 20:04:31: 10000000 INFO @ Sat, 15 Jan 2022 20:04:33: 3000000 INFO @ Sat, 15 Jan 2022 20:04:35: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:04:35: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:04:35: #1 total tags in treatment: 3535830 INFO @ Sat, 15 Jan 2022 20:04:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:04:35: #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 20:04:35: #1 tags after filtering in treatment: 1824870 INFO @ Sat, 15 Jan 2022 20:04:35: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 15 Jan 2022 20:04:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:04:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:04:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:04:35: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:04:35: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:04:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:04:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:04:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:04:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:04:35: #2 predicted fragment length is 61 bps INFO @ Sat, 15 Jan 2022 20:04:35: #2 alternative fragment length(s) may be 27,61,132,186,220,243,265,288,309,354,357,397,424,430,480,486,509,531,547,565 bps INFO @ Sat, 15 Jan 2022 20:04:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.10_model.r WARNING @ Sat, 15 Jan 2022 20:04:35: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:04:35: #2 You may need to consider one of the other alternative d(s): 27,61,132,186,220,243,265,288,309,354,357,397,424,430,480,486,509,531,547,565 WARNING @ Sat, 15 Jan 2022 20:04:35: #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 20:04:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:04:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:04:37: 4000000 INFO @ Sat, 15 Jan 2022 20:04:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:04:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:04:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:04:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.10_summits.bed INFO @ Sat, 15 Jan 2022 20:04:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:04:41: 5000000 INFO @ Sat, 15 Jan 2022 20:04:45: 6000000 INFO @ Sat, 15 Jan 2022 20:04:49: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:04:53: 8000000 INFO @ Sat, 15 Jan 2022 20:04:57: 9000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:05:01: 10000000 INFO @ Sat, 15 Jan 2022 20:05:05: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:05:05: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:05:05: #1 total tags in treatment: 3535830 INFO @ Sat, 15 Jan 2022 20:05:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:05:05: #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 20:05:05: #1 tags after filtering in treatment: 1824870 INFO @ Sat, 15 Jan 2022 20:05:05: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 15 Jan 2022 20:05:05: #1 finished! INFO @ Sat, 15 Jan 2022 20:05:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:05:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:05:05: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:05:05: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:05:05: start model_add_line... INFO @ Sat, 15 Jan 2022 20:05:05: start X-correlation... INFO @ Sat, 15 Jan 2022 20:05:05: end of X-cor INFO @ Sat, 15 Jan 2022 20:05:05: #2 finished! INFO @ Sat, 15 Jan 2022 20:05:05: #2 predicted fragment length is 61 bps INFO @ Sat, 15 Jan 2022 20:05:05: #2 alternative fragment length(s) may be 27,61,132,186,220,243,265,288,309,354,357,397,424,430,480,486,509,531,547,565 bps INFO @ Sat, 15 Jan 2022 20:05:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.20_model.r WARNING @ Sat, 15 Jan 2022 20:05:05: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:05:05: #2 You may need to consider one of the other alternative d(s): 27,61,132,186,220,243,265,288,309,354,357,397,424,430,480,486,509,531,547,565 WARNING @ Sat, 15 Jan 2022 20:05:05: #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 20:05:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:05:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:05:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:05:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:05:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:05:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245400/SRX8245400.20_summits.bed INFO @ Sat, 15 Jan 2022 20:05:10: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling