Job ID = 8070411 SRX = SRX8392415 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:15:28 8227270 reads; of these: 8227270 (100.00%) were paired; of these: 2231306 (27.12%) aligned concordantly 0 times 5116910 (62.19%) aligned concordantly exactly 1 time 879054 (10.68%) aligned concordantly >1 times ---- 2231306 pairs aligned concordantly 0 times; of these: 917843 (41.13%) aligned discordantly 1 time ---- 1313463 pairs aligned 0 times concordantly or discordantly; of these: 2626926 mates make up the pairs; of these: 2319255 (88.29%) aligned 0 times 137776 (5.24%) aligned exactly 1 time 169895 (6.47%) aligned >1 times 85.91% overall alignment rate Time searching: 00:15:28 Overall time: 00:15:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 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 chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1050840 / 6859018 = 0.1532 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:26:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.bam'] # control file = None # effective genome size = 9.00e+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, 08 Aug 2020 13:26:38: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:38: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:45: 1000000 INFO @ Sat, 08 Aug 2020 13:26:52: 2000000 INFO @ Sat, 08 Aug 2020 13:26:59: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:27:06: 4000000 INFO @ Sat, 08 Aug 2020 13:27:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.bam'] # control file = None # effective genome size = 9.00e+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, 08 Aug 2020 13:27:08: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:08: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:14: 5000000 INFO @ Sat, 08 Aug 2020 13:27:17: 1000000 INFO @ Sat, 08 Aug 2020 13:27:22: 6000000 INFO @ Sat, 08 Aug 2020 13:27:25: 2000000 INFO @ Sat, 08 Aug 2020 13:27:29: 7000000 INFO @ Sat, 08 Aug 2020 13:27:33: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:27:37: 8000000 INFO @ Sat, 08 Aug 2020 13:27:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.bam'] # control file = None # effective genome size = 9.00e+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, 08 Aug 2020 13:27:38: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:38: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:42: 4000000 INFO @ Sat, 08 Aug 2020 13:27:44: 9000000 INFO @ Sat, 08 Aug 2020 13:27:46: 1000000 INFO @ Sat, 08 Aug 2020 13:27:50: 5000000 INFO @ Sat, 08 Aug 2020 13:27:52: 10000000 INFO @ Sat, 08 Aug 2020 13:27:53: 2000000 INFO @ Sat, 08 Aug 2020 13:27:59: 6000000 INFO @ Sat, 08 Aug 2020 13:28:00: 11000000 INFO @ Sat, 08 Aug 2020 13:28:01: 3000000 INFO @ Sat, 08 Aug 2020 13:28:07: 12000000 INFO @ Sat, 08 Aug 2020 13:28:07: 7000000 INFO @ Sat, 08 Aug 2020 13:28:07: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:07: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:07: #1 total tags in treatment: 5057386 INFO @ Sat, 08 Aug 2020 13:28:07: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:28:07: #1 tags after filtering in treatment: 4708161 INFO @ Sat, 08 Aug 2020 13:28:07: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:28:07: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:07: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:08: #2 number of paired peaks: 451 WARNING @ Sat, 08 Aug 2020 13:28:08: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sat, 08 Aug 2020 13:28:08: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:08: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:08: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:08: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:08: #2 predicted fragment length is 199 bps INFO @ Sat, 08 Aug 2020 13:28:08: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 08 Aug 2020 13:28:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.05_model.r WARNING @ Sat, 08 Aug 2020 13:28:08: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:08: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 08 Aug 2020 13:28:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:28:08: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:28:08: 4000000 INFO @ Sat, 08 Aug 2020 13:28:16: 8000000 INFO @ Sat, 08 Aug 2020 13:28:16: 5000000 INFO @ Sat, 08 Aug 2020 13:28:19: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:23: 6000000 INFO @ Sat, 08 Aug 2020 13:28:24: 9000000 INFO @ Sat, 08 Aug 2020 13:28:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.05_summits.bed INFO @ Sat, 08 Aug 2020 13:28:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (346 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:28:31: 7000000 INFO @ Sat, 08 Aug 2020 13:28:33: 10000000 INFO @ Sat, 08 Aug 2020 13:28:38: 8000000 INFO @ Sat, 08 Aug 2020 13:28:41: 11000000 INFO @ Sat, 08 Aug 2020 13:28:45: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:28:50: 12000000 INFO @ Sat, 08 Aug 2020 13:28:50: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:50: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:50: #1 total tags in treatment: 5057386 INFO @ Sat, 08 Aug 2020 13:28:50: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:28:50: #1 tags after filtering in treatment: 4708161 INFO @ Sat, 08 Aug 2020 13:28:50: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:28:50: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:50: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:50: #2 number of paired peaks: 451 WARNING @ Sat, 08 Aug 2020 13:28:50: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sat, 08 Aug 2020 13:28:50: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:50: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:50: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:50: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:50: #2 predicted fragment length is 199 bps INFO @ Sat, 08 Aug 2020 13:28:50: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 08 Aug 2020 13:28:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.10_model.r WARNING @ Sat, 08 Aug 2020 13:28:50: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:50: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 08 Aug 2020 13:28:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:28:50: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:28:52: 10000000 INFO @ Sat, 08 Aug 2020 13:28:59: 11000000 INFO @ Sat, 08 Aug 2020 13:29:01: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.10_summits.bed INFO @ Sat, 08 Aug 2020 13:29:06: Done! INFO @ Sat, 08 Aug 2020 13:29:06: 12000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:29:06: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:29:06: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:29:06: #1 total tags in treatment: 5057386 INFO @ Sat, 08 Aug 2020 13:29:06: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:29:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:29:06: #1 tags after filtering in treatment: 4708161 INFO @ Sat, 08 Aug 2020 13:29:06: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:29:06: #1 finished! INFO @ Sat, 08 Aug 2020 13:29:06: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:29:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:29:07: #2 number of paired peaks: 451 WARNING @ Sat, 08 Aug 2020 13:29:07: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sat, 08 Aug 2020 13:29:07: start model_add_line... INFO @ Sat, 08 Aug 2020 13:29:07: start X-correlation... INFO @ Sat, 08 Aug 2020 13:29:07: end of X-cor INFO @ Sat, 08 Aug 2020 13:29:07: #2 finished! INFO @ Sat, 08 Aug 2020 13:29:07: #2 predicted fragment length is 199 bps INFO @ Sat, 08 Aug 2020 13:29:07: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 08 Aug 2020 13:29:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.20_model.r WARNING @ Sat, 08 Aug 2020 13:29:07: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:29:07: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 08 Aug 2020 13:29:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:29:07: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:29:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:29:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392415/SRX8392415.20_summits.bed INFO @ Sat, 08 Aug 2020 13:29:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 millis CompletedMACS2peakCalling