Job ID = 8070444 SRX = SRX7217790 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: 00:15:35 8389572 reads; of these: 8389572 (100.00%) were paired; of these: 1326103 (15.81%) aligned concordantly 0 times 6023772 (71.80%) aligned concordantly exactly 1 time 1039697 (12.39%) aligned concordantly >1 times ---- 1326103 pairs aligned concordantly 0 times; of these: 472603 (35.64%) aligned discordantly 1 time ---- 853500 pairs aligned 0 times concordantly or discordantly; of these: 1707000 mates make up the pairs; of these: 1466766 (85.93%) aligned 0 times 102529 (6.01%) aligned exactly 1 time 137705 (8.07%) aligned >1 times 91.26% overall alignment rate Time searching: 00:15:35 Overall time: 00:15:35 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] 2130036 / 7500757 = 0.2840 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 13:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.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 13:27:21: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:21: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:29: 1000000 INFO @ Sat, 08 Aug 2020 13:27:36: 2000000 INFO @ Sat, 08 Aug 2020 13:27:43: 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 13:27:50: 4000000 INFO @ Sat, 08 Aug 2020 13:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.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 13:27:51: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:51: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:58: 5000000 INFO @ Sat, 08 Aug 2020 13:27:59: 1000000 INFO @ Sat, 08 Aug 2020 13:28:06: 6000000 INFO @ Sat, 08 Aug 2020 13:28:07: 2000000 INFO @ Sat, 08 Aug 2020 13:28:14: 7000000 INFO @ Sat, 08 Aug 2020 13:28:15: 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 13:28:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.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 13:28:21: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:28:21: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:28:21: 8000000 INFO @ Sat, 08 Aug 2020 13:28:22: 4000000 INFO @ Sat, 08 Aug 2020 13:28:29: 9000000 INFO @ Sat, 08 Aug 2020 13:28:29: 1000000 INFO @ Sat, 08 Aug 2020 13:28:30: 5000000 INFO @ Sat, 08 Aug 2020 13:28:37: 10000000 INFO @ Sat, 08 Aug 2020 13:28:37: 2000000 INFO @ Sat, 08 Aug 2020 13:28:38: 6000000 INFO @ Sat, 08 Aug 2020 13:28:45: 11000000 INFO @ Sat, 08 Aug 2020 13:28:45: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:45: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:45: #1 total tags in treatment: 4997919 INFO @ Sat, 08 Aug 2020 13:28:45: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:45: #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 13:28:45: #1 tags after filtering in treatment: 4496686 INFO @ Sat, 08 Aug 2020 13:28:45: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:28:45: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:45: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:45: 3000000 INFO @ Sat, 08 Aug 2020 13:28:46: #2 number of paired peaks: 765 WARNING @ Sat, 08 Aug 2020 13:28:46: Fewer paired peaks (765) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 765 pairs to build model! INFO @ Sat, 08 Aug 2020 13:28:46: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:46: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:46: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:46: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:46: #2 predicted fragment length is 212 bps INFO @ Sat, 08 Aug 2020 13:28:46: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 08 Aug 2020 13:28:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.05_model.r WARNING @ Sat, 08 Aug 2020 13:28:46: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:46: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 08 Aug 2020 13:28:46: #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 13:28:46: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:28:46: 7000000 INFO @ Sat, 08 Aug 2020 13:28:53: 4000000 INFO @ Sat, 08 Aug 2020 13:28:54: 8000000 INFO @ Sat, 08 Aug 2020 13:28:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:01: 5000000 INFO @ Sat, 08 Aug 2020 13:29:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.05_summits.bed INFO @ Sat, 08 Aug 2020 13:29:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2365 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:29:03: 9000000 INFO @ Sat, 08 Aug 2020 13:29:09: 6000000 INFO @ Sat, 08 Aug 2020 13:29:11: 10000000 INFO @ Sat, 08 Aug 2020 13:29:17: 7000000 INFO @ Sat, 08 Aug 2020 13:29:19: 11000000 INFO @ Sat, 08 Aug 2020 13:29:20: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:29:20: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:29:20: #1 total tags in treatment: 4997919 INFO @ Sat, 08 Aug 2020 13:29:20: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:29:20: #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 13:29:20: #1 tags after filtering in treatment: 4496686 INFO @ Sat, 08 Aug 2020 13:29:20: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:29:20: #1 finished! INFO @ Sat, 08 Aug 2020 13:29:20: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:29:20: #2 number of paired peaks: 765 WARNING @ Sat, 08 Aug 2020 13:29:20: Fewer paired peaks (765) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 765 pairs to build model! INFO @ Sat, 08 Aug 2020 13:29:20: start model_add_line... INFO @ Sat, 08 Aug 2020 13:29:20: start X-correlation... INFO @ Sat, 08 Aug 2020 13:29:20: end of X-cor INFO @ Sat, 08 Aug 2020 13:29:20: #2 finished! INFO @ Sat, 08 Aug 2020 13:29:20: #2 predicted fragment length is 212 bps INFO @ Sat, 08 Aug 2020 13:29:20: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 08 Aug 2020 13:29:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.10_model.r WARNING @ Sat, 08 Aug 2020 13:29:20: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:29:20: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 08 Aug 2020 13:29:20: #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 13:29:20: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:29:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:29:25: 8000000 INFO @ Sat, 08 Aug 2020 13:29:31: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:33: 9000000 INFO @ Sat, 08 Aug 2020 13:29:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.10_summits.bed INFO @ Sat, 08 Aug 2020 13:29:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1129 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:29:40: 10000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:29:48: 11000000 INFO @ Sat, 08 Aug 2020 13:29:48: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:29:48: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:29:48: #1 total tags in treatment: 4997919 INFO @ Sat, 08 Aug 2020 13:29:48: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:29:48: #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 13:29:48: #1 tags after filtering in treatment: 4496686 INFO @ Sat, 08 Aug 2020 13:29:48: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:29:48: #1 finished! INFO @ Sat, 08 Aug 2020 13:29:48: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:29:49: #2 number of paired peaks: 765 WARNING @ Sat, 08 Aug 2020 13:29:49: Fewer paired peaks (765) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 765 pairs to build model! INFO @ Sat, 08 Aug 2020 13:29:49: start model_add_line... INFO @ Sat, 08 Aug 2020 13:29:49: start X-correlation... INFO @ Sat, 08 Aug 2020 13:29:49: end of X-cor INFO @ Sat, 08 Aug 2020 13:29:49: #2 finished! INFO @ Sat, 08 Aug 2020 13:29:49: #2 predicted fragment length is 212 bps INFO @ Sat, 08 Aug 2020 13:29:49: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 08 Aug 2020 13:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.20_model.r WARNING @ Sat, 08 Aug 2020 13:29:49: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:29:49: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 08 Aug 2020 13:29:49: #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 13:29:49: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:30:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217790/SRX7217790.20_summits.bed INFO @ Sat, 08 Aug 2020 13:30:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (472 records, 4 fields): 2 millis CompletedMACS2peakCalling