Job ID = 6367847 SRX = SRX4085415 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:37:44 prefetch.2.10.7: 1) Downloading 'SRR7167444'... 2020-06-15T23:37:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:46 prefetch.2.10.7: 1) 'SRR7167444' was downloaded successfully Read 14884254 spots for SRR7167444/SRR7167444.sra Written 14884254 spots for SRR7167444/SRR7167444.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: 00:07:12 14884254 reads; of these: 14884254 (100.00%) were paired; of these: 11394917 (76.56%) aligned concordantly 0 times 3032391 (20.37%) aligned concordantly exactly 1 time 456946 (3.07%) aligned concordantly >1 times ---- 11394917 pairs aligned concordantly 0 times; of these: 214042 (1.88%) aligned discordantly 1 time ---- 11180875 pairs aligned 0 times concordantly or discordantly; of these: 22361750 mates make up the pairs; of these: 15504833 (69.34%) aligned 0 times 6068595 (27.14%) aligned exactly 1 time 788322 (3.53%) aligned >1 times 47.92% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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 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 chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 237683 / 3575803 = 0.0665 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 08:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.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 08:55:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:51: 1000000 INFO @ Tue, 16 Jun 2020 08:55:58: 2000000 INFO @ Tue, 16 Jun 2020 08:56:05: 3000000 INFO @ Tue, 16 Jun 2020 08:56:11: 4000000 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 08:56:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.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 08:56:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:19: 5000000 INFO @ Tue, 16 Jun 2020 08:56:22: 1000000 INFO @ Tue, 16 Jun 2020 08:56:26: 6000000 INFO @ Tue, 16 Jun 2020 08:56:29: 2000000 INFO @ Tue, 16 Jun 2020 08:56:33: 7000000 INFO @ Tue, 16 Jun 2020 08:56:36: 3000000 INFO @ Tue, 16 Jun 2020 08:56:40: 8000000 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 08:56:43: 4000000 INFO @ Tue, 16 Jun 2020 08:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.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 08:56:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:47: 9000000 INFO @ Tue, 16 Jun 2020 08:56:51: 5000000 INFO @ Tue, 16 Jun 2020 08:56:51: 1000000 INFO @ Tue, 16 Jun 2020 08:56:55: 10000000 INFO @ Tue, 16 Jun 2020 08:56:58: 2000000 INFO @ Tue, 16 Jun 2020 08:56:58: 6000000 INFO @ Tue, 16 Jun 2020 08:57:03: 11000000 INFO @ Tue, 16 Jun 2020 08:57:05: 3000000 INFO @ Tue, 16 Jun 2020 08:57:06: 7000000 INFO @ Tue, 16 Jun 2020 08:57:11: 12000000 INFO @ Tue, 16 Jun 2020 08:57:12: 4000000 INFO @ Tue, 16 Jun 2020 08:57:14: 8000000 INFO @ Tue, 16 Jun 2020 08:57:18: 13000000 INFO @ Tue, 16 Jun 2020 08:57:19: 5000000 INFO @ Tue, 16 Jun 2020 08:57:21: 9000000 INFO @ Tue, 16 Jun 2020 08:57:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:57:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:57:24: #1 total tags in treatment: 3255486 INFO @ Tue, 16 Jun 2020 08:57:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:24: #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 08:57:24: #1 tags after filtering in treatment: 3058285 INFO @ Tue, 16 Jun 2020 08:57:24: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 08:57:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:24: #2 number of paired peaks: 186 WARNING @ Tue, 16 Jun 2020 08:57:24: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:24: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 08:57:24: #2 alternative fragment length(s) may be 93,140,166 bps INFO @ Tue, 16 Jun 2020 08:57:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.05_model.r WARNING @ Tue, 16 Jun 2020 08:57:24: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:24: #2 You may need to consider one of the other alternative d(s): 93,140,166 WARNING @ Tue, 16 Jun 2020 08:57:24: #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 08:57:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:26: 6000000 INFO @ Tue, 16 Jun 2020 08:57:29: 10000000 INFO @ Tue, 16 Jun 2020 08:57:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:32: 7000000 INFO @ Tue, 16 Jun 2020 08:57:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:36: 11000000 INFO @ Tue, 16 Jun 2020 08:57:39: 8000000 INFO @ Tue, 16 Jun 2020 08:57:43: 12000000 INFO @ Tue, 16 Jun 2020 08:57:46: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:57:50: 13000000 INFO @ Tue, 16 Jun 2020 08:57:53: 10000000 INFO @ Tue, 16 Jun 2020 08:57:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:57:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:57:56: #1 total tags in treatment: 3255486 INFO @ Tue, 16 Jun 2020 08:57:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:56: #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 08:57:56: #1 tags after filtering in treatment: 3058285 INFO @ Tue, 16 Jun 2020 08:57:56: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 08:57:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:56: #2 number of paired peaks: 186 WARNING @ Tue, 16 Jun 2020 08:57:56: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:56: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 08:57:56: #2 alternative fragment length(s) may be 93,140,166 bps INFO @ Tue, 16 Jun 2020 08:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.10_model.r WARNING @ Tue, 16 Jun 2020 08:57:56: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:56: #2 You may need to consider one of the other alternative d(s): 93,140,166 WARNING @ Tue, 16 Jun 2020 08:57:56: #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 08:57:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:59: 11000000 INFO @ Tue, 16 Jun 2020 08:58:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:04: 12000000 INFO @ Tue, 16 Jun 2020 08:58:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:10: 13000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:58:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:58:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:58:14: #1 total tags in treatment: 3255486 INFO @ Tue, 16 Jun 2020 08:58:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:14: #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 08:58:14: #1 tags after filtering in treatment: 3058285 INFO @ Tue, 16 Jun 2020 08:58:14: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 08:58:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:14: #2 number of paired peaks: 186 WARNING @ Tue, 16 Jun 2020 08:58:14: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:14: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 08:58:14: #2 alternative fragment length(s) may be 93,140,166 bps INFO @ Tue, 16 Jun 2020 08:58:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.20_model.r WARNING @ Tue, 16 Jun 2020 08:58:14: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:58:14: #2 You may need to consider one of the other alternative d(s): 93,140,166 WARNING @ Tue, 16 Jun 2020 08:58:14: #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 08:58:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085415/SRX4085415.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 1 millis CompletedMACS2peakCalling