Job ID = 14521264 SRX = SRX8245393 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8247314 spots for SRR11684604/SRR11684604.sra Written 8247314 spots for SRR11684604/SRR11684604.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: 00:04:45 8247314 reads; of these: 8247314 (100.00%) were paired; of these: 4603650 (55.82%) aligned concordantly 0 times 3189623 (38.67%) aligned concordantly exactly 1 time 454041 (5.51%) aligned concordantly >1 times ---- 4603650 pairs aligned concordantly 0 times; of these: 11205 (0.24%) aligned discordantly 1 time ---- 4592445 pairs aligned 0 times concordantly or discordantly; of these: 9184890 mates make up the pairs; of these: 5279441 (57.48%) aligned 0 times 3378342 (36.78%) aligned exactly 1 time 527107 (5.74%) aligned >1 times 67.99% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 154393 / 3654318 = 0.0422 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 20:53:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.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 20:53:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:53:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:03: 1000000 INFO @ Sat, 15 Jan 2022 20:54:07: 2000000 INFO @ Sat, 15 Jan 2022 20:54:12: 3000000 INFO @ Sat, 15 Jan 2022 20:54:17: 4000000 INFO @ Sat, 15 Jan 2022 20:54:21: 5000000 INFO @ Sat, 15 Jan 2022 20:54:26: 6000000 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 20:54:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.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 20:54:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:31: 7000000 INFO @ Sat, 15 Jan 2022 20:54:33: 1000000 INFO @ Sat, 15 Jan 2022 20:54:36: 8000000 INFO @ Sat, 15 Jan 2022 20:54:39: 2000000 INFO @ Sat, 15 Jan 2022 20:54:42: 9000000 INFO @ Sat, 15 Jan 2022 20:54:45: 3000000 INFO @ Sat, 15 Jan 2022 20:54:47: 10000000 INFO @ Sat, 15 Jan 2022 20:54:51: 4000000 INFO @ Sat, 15 Jan 2022 20:54:52: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:54:52: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:54:52: #1 total tags in treatment: 3489627 INFO @ Sat, 15 Jan 2022 20:54:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:54:52: #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 20:54:52: #1 tags after filtering in treatment: 2158196 INFO @ Sat, 15 Jan 2022 20:54:52: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 20:54:52: #1 finished! INFO @ Sat, 15 Jan 2022 20:54:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:54:53: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:54:53: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:54:53: start model_add_line... INFO @ Sat, 15 Jan 2022 20:54:53: start X-correlation... INFO @ Sat, 15 Jan 2022 20:54:53: end of X-cor INFO @ Sat, 15 Jan 2022 20:54:53: #2 finished! INFO @ Sat, 15 Jan 2022 20:54:53: #2 predicted fragment length is 52 bps INFO @ Sat, 15 Jan 2022 20:54:53: #2 alternative fragment length(s) may be 52,110,145,176,201,221,263,284,312,368,384,423,474,496,501,519,532,587,595 bps INFO @ Sat, 15 Jan 2022 20:54:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.05_model.r WARNING @ Sat, 15 Jan 2022 20:54:53: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:54:53: #2 You may need to consider one of the other alternative d(s): 52,110,145,176,201,221,263,284,312,368,384,423,474,496,501,519,532,587,595 WARNING @ Sat, 15 Jan 2022 20:54:53: #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 20:54:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:54:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:54:56: 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 20:54:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.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 20:54:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:54:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:54:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.05_summits.bed INFO @ Sat, 15 Jan 2022 20:54:58: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:55:01: 6000000 INFO @ Sat, 15 Jan 2022 20:55:04: 1000000 INFO @ Sat, 15 Jan 2022 20:55:07: 7000000 INFO @ Sat, 15 Jan 2022 20:55:11: 2000000 INFO @ Sat, 15 Jan 2022 20:55:12: 8000000 INFO @ Sat, 15 Jan 2022 20:55:17: 3000000 INFO @ Sat, 15 Jan 2022 20:55:18: 9000000 INFO @ Sat, 15 Jan 2022 20:55:23: 4000000 INFO @ Sat, 15 Jan 2022 20:55:24: 10000000 INFO @ Sat, 15 Jan 2022 20:55:29: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:55:29: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:55:29: #1 total tags in treatment: 3489627 INFO @ Sat, 15 Jan 2022 20:55:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:55:29: #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 20:55:29: #1 tags after filtering in treatment: 2158196 INFO @ Sat, 15 Jan 2022 20:55:29: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 20:55:29: #1 finished! INFO @ Sat, 15 Jan 2022 20:55:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:55:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:55:29: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:55:29: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:55:29: start model_add_line... INFO @ Sat, 15 Jan 2022 20:55:29: start X-correlation... INFO @ Sat, 15 Jan 2022 20:55:29: end of X-cor INFO @ Sat, 15 Jan 2022 20:55:29: #2 finished! INFO @ Sat, 15 Jan 2022 20:55:29: #2 predicted fragment length is 52 bps INFO @ Sat, 15 Jan 2022 20:55:29: #2 alternative fragment length(s) may be 52,110,145,176,201,221,263,284,312,368,384,423,474,496,501,519,532,587,595 bps INFO @ Sat, 15 Jan 2022 20:55:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.10_model.r WARNING @ Sat, 15 Jan 2022 20:55:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:55:29: #2 You may need to consider one of the other alternative d(s): 52,110,145,176,201,221,263,284,312,368,384,423,474,496,501,519,532,587,595 WARNING @ Sat, 15 Jan 2022 20:55:29: #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 20:55:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:55:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:55:30: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:55:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:55:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:55:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:55:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.10_summits.bed INFO @ Sat, 15 Jan 2022 20:55:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:55:36: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:55:42: 7000000 INFO @ Sat, 15 Jan 2022 20:55:48: 8000000 INFO @ Sat, 15 Jan 2022 20:55:54: 9000000 INFO @ Sat, 15 Jan 2022 20:56:00: 10000000 INFO @ Sat, 15 Jan 2022 20:56:05: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:56:05: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:56:05: #1 total tags in treatment: 3489627 INFO @ Sat, 15 Jan 2022 20:56:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:56:05: #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 20:56:05: #1 tags after filtering in treatment: 2158196 INFO @ Sat, 15 Jan 2022 20:56:05: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 20:56:05: #1 finished! INFO @ Sat, 15 Jan 2022 20:56:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:56:05: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:56:05: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:56:05: start model_add_line... INFO @ Sat, 15 Jan 2022 20:56:05: start X-correlation... INFO @ Sat, 15 Jan 2022 20:56:05: end of X-cor INFO @ Sat, 15 Jan 2022 20:56:05: #2 finished! INFO @ Sat, 15 Jan 2022 20:56:05: #2 predicted fragment length is 52 bps INFO @ Sat, 15 Jan 2022 20:56:05: #2 alternative fragment length(s) may be 52,110,145,176,201,221,263,284,312,368,384,423,474,496,501,519,532,587,595 bps INFO @ Sat, 15 Jan 2022 20:56:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.20_model.r WARNING @ Sat, 15 Jan 2022 20:56:05: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:56:05: #2 You may need to consider one of the other alternative d(s): 52,110,145,176,201,221,263,284,312,368,384,423,474,496,501,519,532,587,595 WARNING @ Sat, 15 Jan 2022 20:56:05: #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 20:56:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:56:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:56:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:56:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:56:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:56:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245393/SRX8245393.20_summits.bed INFO @ Sat, 15 Jan 2022 20:56:11: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 13 millis CompletedMACS2peakCalling