Job ID = 6507796 SRX = SRX4085423 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:16:03 prefetch.2.10.7: 1) Downloading 'SRR7167452'... 2020-06-26T13:16:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:19:38 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:19:38 prefetch.2.10.7: 1) 'SRR7167452' was downloaded successfully Read 14065771 spots for SRR7167452/SRR7167452.sra Written 14065771 spots for SRR7167452/SRR7167452.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:32 14065771 reads; of these: 14065771 (100.00%) were paired; of these: 10509064 (74.71%) aligned concordantly 0 times 3041119 (21.62%) aligned concordantly exactly 1 time 515588 (3.67%) aligned concordantly >1 times ---- 10509064 pairs aligned concordantly 0 times; of these: 270104 (2.57%) aligned discordantly 1 time ---- 10238960 pairs aligned 0 times concordantly or discordantly; of these: 20477920 mates make up the pairs; of these: 14050788 (68.61%) aligned 0 times 5770969 (28.18%) aligned exactly 1 time 656163 (3.20%) aligned >1 times 50.05% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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] 321421 / 3688540 = 0.0871 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 @ Fri, 26 Jun 2020 22:33:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.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 @ Fri, 26 Jun 2020 22:33:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:07: 1000000 INFO @ Fri, 26 Jun 2020 22:33:13: 2000000 INFO @ Fri, 26 Jun 2020 22:33:19: 3000000 INFO @ Fri, 26 Jun 2020 22:33:25: 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 @ Fri, 26 Jun 2020 22:33:31: 5000000 INFO @ Fri, 26 Jun 2020 22:33:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.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 @ Fri, 26 Jun 2020 22:33:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:37: 6000000 INFO @ Fri, 26 Jun 2020 22:33:38: 1000000 INFO @ Fri, 26 Jun 2020 22:33:44: 7000000 INFO @ Fri, 26 Jun 2020 22:33:45: 2000000 INFO @ Fri, 26 Jun 2020 22:33:50: 8000000 INFO @ Fri, 26 Jun 2020 22:33:51: 3000000 INFO @ Fri, 26 Jun 2020 22:33:56: 9000000 INFO @ Fri, 26 Jun 2020 22:33:57: 4000000 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 @ Fri, 26 Jun 2020 22:34:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.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 @ Fri, 26 Jun 2020 22:34:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:34:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:34:03: 10000000 INFO @ Fri, 26 Jun 2020 22:34:04: 5000000 INFO @ Fri, 26 Jun 2020 22:34:10: 11000000 INFO @ Fri, 26 Jun 2020 22:34:10: 1000000 INFO @ Fri, 26 Jun 2020 22:34:10: 6000000 INFO @ Fri, 26 Jun 2020 22:34:17: 12000000 INFO @ Fri, 26 Jun 2020 22:34:17: 7000000 INFO @ Fri, 26 Jun 2020 22:34:19: 2000000 INFO @ Fri, 26 Jun 2020 22:34:23: 13000000 INFO @ Fri, 26 Jun 2020 22:34:24: 8000000 INFO @ Fri, 26 Jun 2020 22:34:26: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:34:26: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:34:26: #1 total tags in treatment: 3244171 INFO @ Fri, 26 Jun 2020 22:34:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:34:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:34:26: #1 tags after filtering in treatment: 2956935 INFO @ Fri, 26 Jun 2020 22:34:26: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:34:26: #1 finished! INFO @ Fri, 26 Jun 2020 22:34:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:34:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:34:26: #2 number of paired peaks: 514 WARNING @ Fri, 26 Jun 2020 22:34:26: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Fri, 26 Jun 2020 22:34:26: start model_add_line... INFO @ Fri, 26 Jun 2020 22:34:26: start X-correlation... INFO @ Fri, 26 Jun 2020 22:34:26: end of X-cor INFO @ Fri, 26 Jun 2020 22:34:26: #2 finished! INFO @ Fri, 26 Jun 2020 22:34:26: #2 predicted fragment length is 82 bps INFO @ Fri, 26 Jun 2020 22:34:26: #2 alternative fragment length(s) may be 82 bps INFO @ Fri, 26 Jun 2020 22:34:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.05_model.r WARNING @ Fri, 26 Jun 2020 22:34:26: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:34:26: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Fri, 26 Jun 2020 22:34:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:34:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:34:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:34:27: 3000000 INFO @ Fri, 26 Jun 2020 22:34:31: 9000000 INFO @ Fri, 26 Jun 2020 22:34:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:34:35: 4000000 INFO @ Fri, 26 Jun 2020 22:34:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:34:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:34:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.05_summits.bed INFO @ Fri, 26 Jun 2020 22:34:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2174 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:34:38: 10000000 INFO @ Fri, 26 Jun 2020 22:34:43: 5000000 INFO @ Fri, 26 Jun 2020 22:34:45: 11000000 INFO @ Fri, 26 Jun 2020 22:34:51: 6000000 INFO @ Fri, 26 Jun 2020 22:34:51: 12000000 INFO @ Fri, 26 Jun 2020 22:34:57: 13000000 INFO @ Fri, 26 Jun 2020 22:34:59: 7000000 INFO @ Fri, 26 Jun 2020 22:35:00: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:35:00: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:35:00: #1 total tags in treatment: 3244171 INFO @ Fri, 26 Jun 2020 22:35:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:35:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:35:00: #1 tags after filtering in treatment: 2956935 INFO @ Fri, 26 Jun 2020 22:35:00: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:35:00: #1 finished! INFO @ Fri, 26 Jun 2020 22:35:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:35:00: #2 number of paired peaks: 514 WARNING @ Fri, 26 Jun 2020 22:35:00: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Fri, 26 Jun 2020 22:35:00: start model_add_line... INFO @ Fri, 26 Jun 2020 22:35:00: start X-correlation... INFO @ Fri, 26 Jun 2020 22:35:00: end of X-cor INFO @ Fri, 26 Jun 2020 22:35:00: #2 finished! INFO @ Fri, 26 Jun 2020 22:35:00: #2 predicted fragment length is 82 bps INFO @ Fri, 26 Jun 2020 22:35:00: #2 alternative fragment length(s) may be 82 bps INFO @ Fri, 26 Jun 2020 22:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.10_model.r WARNING @ Fri, 26 Jun 2020 22:35:00: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:35:00: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Fri, 26 Jun 2020 22:35:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:35:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:35:07: 8000000 INFO @ Fri, 26 Jun 2020 22:35:07: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:35:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:35:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:35:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.10_summits.bed INFO @ Fri, 26 Jun 2020 22:35:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (831 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:35:14: 9000000 INFO @ Fri, 26 Jun 2020 22:35:22: 10000000 INFO @ Fri, 26 Jun 2020 22:35:29: 11000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:35:36: 12000000 INFO @ Fri, 26 Jun 2020 22:35:43: 13000000 INFO @ Fri, 26 Jun 2020 22:35:46: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:35:46: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:35:46: #1 total tags in treatment: 3244171 INFO @ Fri, 26 Jun 2020 22:35:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:35:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:35:46: #1 tags after filtering in treatment: 2956935 INFO @ Fri, 26 Jun 2020 22:35:46: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:35:46: #1 finished! INFO @ Fri, 26 Jun 2020 22:35:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:35:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:35:47: #2 number of paired peaks: 514 WARNING @ Fri, 26 Jun 2020 22:35:47: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Fri, 26 Jun 2020 22:35:47: start model_add_line... INFO @ Fri, 26 Jun 2020 22:35:47: start X-correlation... INFO @ Fri, 26 Jun 2020 22:35:47: end of X-cor INFO @ Fri, 26 Jun 2020 22:35:47: #2 finished! INFO @ Fri, 26 Jun 2020 22:35:47: #2 predicted fragment length is 82 bps INFO @ Fri, 26 Jun 2020 22:35:47: #2 alternative fragment length(s) may be 82 bps INFO @ Fri, 26 Jun 2020 22:35:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.20_model.r WARNING @ Fri, 26 Jun 2020 22:35:47: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:35:47: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Fri, 26 Jun 2020 22:35:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:35:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:35:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:35:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:35:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:35:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:35:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085423/SRX4085423.20_summits.bed INFO @ Fri, 26 Jun 2020 22:35:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 3 millis CompletedMACS2peakCalling