Job ID = 6367660 SRX = SRX3733154 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:49:03 prefetch.2.10.7: 1) Downloading 'SRR6760667'... 2020-06-15T23:49:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:55:49 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:55:49 prefetch.2.10.7: 1) 'SRR6760667' was downloaded successfully 2020-06-15T23:55:49 prefetch.2.10.7: 'SRR6760667' has 0 unresolved dependencies Read 26843545 spots for SRR6760667/SRR6760667.sra Written 26843545 spots for SRR6760667/SRR6760667.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: 00:43:31 26843545 reads; of these: 26843545 (100.00%) were paired; of these: 1821892 (6.79%) aligned concordantly 0 times 22197630 (82.69%) aligned concordantly exactly 1 time 2824023 (10.52%) aligned concordantly >1 times ---- 1821892 pairs aligned concordantly 0 times; of these: 493739 (27.10%) aligned discordantly 1 time ---- 1328153 pairs aligned 0 times concordantly or discordantly; of these: 2656306 mates make up the pairs; of these: 1958953 (73.75%) aligned 0 times 444986 (16.75%) aligned exactly 1 time 252367 (9.50%) aligned >1 times 96.35% overall alignment rate Time searching: 00:43:31 Overall time: 00:43:31 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 24 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] 18426191 / 25485759 = 0.7230 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 @ Tue, 16 Jun 2020 09:56:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.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 @ Tue, 16 Jun 2020 09:56:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:45: 1000000 INFO @ Tue, 16 Jun 2020 09:56:51: 2000000 INFO @ Tue, 16 Jun 2020 09:56:56: 3000000 INFO @ Tue, 16 Jun 2020 09:57:01: 4000000 INFO @ Tue, 16 Jun 2020 09:57:06: 5000000 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 @ Tue, 16 Jun 2020 09:57:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.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 @ Tue, 16 Jun 2020 09:57:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:57:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:57:12: 6000000 INFO @ Tue, 16 Jun 2020 09:57:16: 1000000 INFO @ Tue, 16 Jun 2020 09:57:17: 7000000 INFO @ Tue, 16 Jun 2020 09:57:21: 2000000 INFO @ Tue, 16 Jun 2020 09:57:23: 8000000 INFO @ Tue, 16 Jun 2020 09:57:27: 3000000 INFO @ Tue, 16 Jun 2020 09:57:28: 9000000 INFO @ Tue, 16 Jun 2020 09:57:33: 4000000 INFO @ Tue, 16 Jun 2020 09:57:34: 10000000 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 @ Tue, 16 Jun 2020 09:57:38: 5000000 INFO @ Tue, 16 Jun 2020 09:57:39: 11000000 INFO @ Tue, 16 Jun 2020 09:57:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.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 @ Tue, 16 Jun 2020 09:57:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:57:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:57:44: 6000000 INFO @ Tue, 16 Jun 2020 09:57:45: 12000000 INFO @ Tue, 16 Jun 2020 09:57:47: 1000000 INFO @ Tue, 16 Jun 2020 09:57:50: 7000000 INFO @ Tue, 16 Jun 2020 09:57:51: 13000000 INFO @ Tue, 16 Jun 2020 09:57:55: 2000000 INFO @ Tue, 16 Jun 2020 09:57:55: 8000000 INFO @ Tue, 16 Jun 2020 09:57:56: 14000000 INFO @ Tue, 16 Jun 2020 09:58:01: 9000000 INFO @ Tue, 16 Jun 2020 09:58:01: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:58:01: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:58:01: #1 total tags in treatment: 6843391 INFO @ Tue, 16 Jun 2020 09:58:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:58:01: #1 tags after filtering in treatment: 5474152 INFO @ Tue, 16 Jun 2020 09:58:01: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 09:58:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:58:02: #2 number of paired peaks: 699 WARNING @ Tue, 16 Jun 2020 09:58:02: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Tue, 16 Jun 2020 09:58:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:58:02: 3000000 INFO @ Tue, 16 Jun 2020 09:58:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:58:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:58:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:58:02: #2 predicted fragment length is 150 bps INFO @ Tue, 16 Jun 2020 09:58:02: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 16 Jun 2020 09:58:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.05_model.r WARNING @ Tue, 16 Jun 2020 09:58:02: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:58:02: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 16 Jun 2020 09:58:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:58:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:58:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:58:06: 10000000 INFO @ Tue, 16 Jun 2020 09:58:09: 4000000 INFO @ Tue, 16 Jun 2020 09:58:11: 11000000 INFO @ Tue, 16 Jun 2020 09:58:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:16: 5000000 INFO @ Tue, 16 Jun 2020 09:58:17: 12000000 INFO @ Tue, 16 Jun 2020 09:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.05_summits.bed INFO @ Tue, 16 Jun 2020 09:58:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (553 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:58:22: 13000000 INFO @ Tue, 16 Jun 2020 09:58:23: 6000000 INFO @ Tue, 16 Jun 2020 09:58:27: 14000000 INFO @ Tue, 16 Jun 2020 09:58:29: 7000000 INFO @ Tue, 16 Jun 2020 09:58:32: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:58:32: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:58:32: #1 total tags in treatment: 6843391 INFO @ Tue, 16 Jun 2020 09:58:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:58:32: #1 tags after filtering in treatment: 5474152 INFO @ Tue, 16 Jun 2020 09:58:32: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 09:58:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:58:33: #2 number of paired peaks: 699 WARNING @ Tue, 16 Jun 2020 09:58:33: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Tue, 16 Jun 2020 09:58:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:58:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:58:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:58:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:58:33: #2 predicted fragment length is 150 bps INFO @ Tue, 16 Jun 2020 09:58:33: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 16 Jun 2020 09:58:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.10_model.r WARNING @ Tue, 16 Jun 2020 09:58:33: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:58:33: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 16 Jun 2020 09:58:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:58:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:58:36: 8000000 INFO @ Tue, 16 Jun 2020 09:58:42: 9000000 INFO @ Tue, 16 Jun 2020 09:58:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:48: 10000000 INFO @ Tue, 16 Jun 2020 09:58:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.10_summits.bed INFO @ Tue, 16 Jun 2020 09:58:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (387 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:58:54: 11000000 INFO @ Tue, 16 Jun 2020 09:59:00: 12000000 INFO @ Tue, 16 Jun 2020 09:59:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:59:12: 14000000 INFO @ Tue, 16 Jun 2020 09:59:17: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:59:17: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:59:17: #1 total tags in treatment: 6843391 INFO @ Tue, 16 Jun 2020 09:59:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:59:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:59:17: #1 tags after filtering in treatment: 5474152 INFO @ Tue, 16 Jun 2020 09:59:17: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 09:59:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:59:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:59:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:59:18: #2 number of paired peaks: 699 WARNING @ Tue, 16 Jun 2020 09:59:18: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Tue, 16 Jun 2020 09:59:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:59:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:59:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:59:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:59:18: #2 predicted fragment length is 150 bps INFO @ Tue, 16 Jun 2020 09:59:18: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 16 Jun 2020 09:59:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.20_model.r WARNING @ Tue, 16 Jun 2020 09:59:18: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:59:18: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 16 Jun 2020 09:59:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:59:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:59:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:59:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733154/SRX3733154.20_summits.bed INFO @ Tue, 16 Jun 2020 09:59:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (242 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。