Job ID = 12531686 SRX = SRX4555055 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4730546 spots for SRR7696756/SRR7696756.sra Written 4730546 spots for SRR7696756/SRR7696756.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: 00:11:04 4730546 reads; of these: 4730546 (100.00%) were paired; of these: 254878 (5.39%) aligned concordantly 0 times 2532332 (53.53%) aligned concordantly exactly 1 time 1943336 (41.08%) aligned concordantly >1 times ---- 254878 pairs aligned concordantly 0 times; of these: 20607 (8.09%) aligned discordantly 1 time ---- 234271 pairs aligned 0 times concordantly or discordantly; of these: 468542 mates make up the pairs; of these: 367294 (78.39%) aligned 0 times 53588 (11.44%) aligned exactly 1 time 47660 (10.17%) aligned >1 times 96.12% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 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] 605301 / 2123830 = 0.2850 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:24:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.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, 17 Apr 2021 09:24:40: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:24:40: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:24:53: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:25:08: 2000000 INFO @ Sat, 17 Apr 2021 09:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.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, 17 Apr 2021 09:25:11: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:25:11: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:25:23: 1000000 INFO @ Sat, 17 Apr 2021 09:25:30: 3000000 INFO @ Sat, 17 Apr 2021 09:25:36: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.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, 17 Apr 2021 09:25:41: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:25:41: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:25:47: 4000000 INFO @ Sat, 17 Apr 2021 09:25:57: 3000000 INFO @ Sat, 17 Apr 2021 09:25:59: 1000000 INFO @ Sat, 17 Apr 2021 09:26:06: 5000000 INFO @ Sat, 17 Apr 2021 09:26:09: 4000000 INFO @ Sat, 17 Apr 2021 09:26:10: 2000000 INFO @ Sat, 17 Apr 2021 09:26:20: 6000000 INFO @ Sat, 17 Apr 2021 09:26:22: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:26:24: 5000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:26:34: 4000000 INFO @ Sat, 17 Apr 2021 09:26:40: 7000000 INFO @ Sat, 17 Apr 2021 09:26:41: 6000000 INFO @ Sat, 17 Apr 2021 09:26:49: 5000000 INFO @ Sat, 17 Apr 2021 09:26:56: 7000000 INFO @ Sat, 17 Apr 2021 09:26:57: #1 tag size is determined as 89 bps INFO @ Sat, 17 Apr 2021 09:26:57: #1 tag size = 89 INFO @ Sat, 17 Apr 2021 09:26:57: #1 total tags in treatment: 3870962 INFO @ Sat, 17 Apr 2021 09:26:57: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:26:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:26:58: #1 tags after filtering in treatment: 1483268 INFO @ Sat, 17 Apr 2021 09:26:58: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 17 Apr 2021 09:26:58: #1 finished! INFO @ Sat, 17 Apr 2021 09:26:58: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:26:58: #2 number of paired peaks: 175 WARNING @ Sat, 17 Apr 2021 09:26:58: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 17 Apr 2021 09:26:58: start model_add_line... INFO @ Sat, 17 Apr 2021 09:26:58: start X-correlation... INFO @ Sat, 17 Apr 2021 09:26:58: end of X-cor INFO @ Sat, 17 Apr 2021 09:26:58: #2 finished! INFO @ Sat, 17 Apr 2021 09:26:58: #2 predicted fragment length is 35 bps INFO @ Sat, 17 Apr 2021 09:26:58: #2 alternative fragment length(s) may be 4,35 bps INFO @ Sat, 17 Apr 2021 09:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.05_model.r WARNING @ Sat, 17 Apr 2021 09:26:58: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:26:58: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Sat, 17 Apr 2021 09:26:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:26:58: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:26:59: 6000000 INFO @ Sat, 17 Apr 2021 09:27:02: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.05_summits.bed INFO @ Sat, 17 Apr 2021 09:27:04: Done! pass1 - making usageList (17 chroms): 9 millis pass2 - checking and writing primary data (1933 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:27:09: #1 tag size is determined as 89 bps INFO @ Sat, 17 Apr 2021 09:27:09: #1 tag size = 89 INFO @ Sat, 17 Apr 2021 09:27:09: #1 total tags in treatment: 3870962 INFO @ Sat, 17 Apr 2021 09:27:09: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:27:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:27:09: #1 tags after filtering in treatment: 1483268 INFO @ Sat, 17 Apr 2021 09:27:09: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 17 Apr 2021 09:27:09: #1 finished! INFO @ Sat, 17 Apr 2021 09:27:09: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:27:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:27:09: #2 number of paired peaks: 175 WARNING @ Sat, 17 Apr 2021 09:27:09: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 17 Apr 2021 09:27:09: start model_add_line... INFO @ Sat, 17 Apr 2021 09:27:09: start X-correlation... INFO @ Sat, 17 Apr 2021 09:27:09: end of X-cor INFO @ Sat, 17 Apr 2021 09:27:09: #2 finished! INFO @ Sat, 17 Apr 2021 09:27:09: #2 predicted fragment length is 35 bps INFO @ Sat, 17 Apr 2021 09:27:09: #2 alternative fragment length(s) may be 4,35 bps INFO @ Sat, 17 Apr 2021 09:27:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.10_model.r WARNING @ Sat, 17 Apr 2021 09:27:09: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:27:09: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Sat, 17 Apr 2021 09:27:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:27:09: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:27:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:27:13: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:27:15: 7000000 INFO @ Sat, 17 Apr 2021 09:27:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:27:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.10_summits.bed INFO @ Sat, 17 Apr 2021 09:27:16: Done! pass1 - making usageList (17 chroms): 10 millis pass2 - checking and writing primary data (796 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:27:29: #1 tag size is determined as 89 bps INFO @ Sat, 17 Apr 2021 09:27:29: #1 tag size = 89 INFO @ Sat, 17 Apr 2021 09:27:29: #1 total tags in treatment: 3870962 INFO @ Sat, 17 Apr 2021 09:27:29: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:27:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:27:29: #1 tags after filtering in treatment: 1483268 INFO @ Sat, 17 Apr 2021 09:27:29: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 17 Apr 2021 09:27:29: #1 finished! INFO @ Sat, 17 Apr 2021 09:27:29: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:27:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:27:29: #2 number of paired peaks: 175 WARNING @ Sat, 17 Apr 2021 09:27:29: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 17 Apr 2021 09:27:29: start model_add_line... INFO @ Sat, 17 Apr 2021 09:27:29: start X-correlation... INFO @ Sat, 17 Apr 2021 09:27:29: end of X-cor INFO @ Sat, 17 Apr 2021 09:27:29: #2 finished! INFO @ Sat, 17 Apr 2021 09:27:29: #2 predicted fragment length is 35 bps INFO @ Sat, 17 Apr 2021 09:27:29: #2 alternative fragment length(s) may be 4,35 bps INFO @ Sat, 17 Apr 2021 09:27:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.20_model.r WARNING @ Sat, 17 Apr 2021 09:27:29: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:27:29: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Sat, 17 Apr 2021 09:27:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:27:29: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:27:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:27:33: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:27:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:27:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:27:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555055/SRX4555055.20_summits.bed INFO @ Sat, 17 Apr 2021 09:27:35: Done! pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (44 records, 4 fields): 25 millis CompletedMACS2peakCalling