Job ID = 6368625 SRX = SRX5064641 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:14:05 prefetch.2.10.7: 1) Downloading 'SRR8246577'... 2020-06-16T00:14:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:35 prefetch.2.10.7: 1) 'SRR8246577' was downloaded successfully 2020-06-16T00:30:35 prefetch.2.10.7: 'SRR8246577' has 0 unresolved dependencies Read 27454854 spots for SRR8246577/SRR8246577.sra Written 27454854 spots for SRR8246577/SRR8246577.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: 00:16:09 27454854 reads; of these: 27454854 (100.00%) were paired; of these: 21388699 (77.90%) aligned concordantly 0 times 5382206 (19.60%) aligned concordantly exactly 1 time 683949 (2.49%) aligned concordantly >1 times ---- 21388699 pairs aligned concordantly 0 times; of these: 59264 (0.28%) aligned discordantly 1 time ---- 21329435 pairs aligned 0 times concordantly or discordantly; of these: 42658870 mates make up the pairs; of these: 42334641 (99.24%) aligned 0 times 261069 (0.61%) aligned exactly 1 time 63160 (0.15%) aligned >1 times 22.90% overall alignment rate Time searching: 00:16:09 Overall time: 00:16:09 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] 2725909 / 6116496 = 0.4457 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 09:54:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.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 09:54:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:40: 1000000 INFO @ Tue, 16 Jun 2020 09:54:46: 2000000 INFO @ Tue, 16 Jun 2020 09:54:52: 3000000 INFO @ Tue, 16 Jun 2020 09:54:58: 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 09:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.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 09:55:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:04: 5000000 INFO @ Tue, 16 Jun 2020 09:55:10: 6000000 INFO @ Tue, 16 Jun 2020 09:55:11: 1000000 INFO @ Tue, 16 Jun 2020 09:55:17: 7000000 INFO @ Tue, 16 Jun 2020 09:55:18: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 09:55:18: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 09:55:18: #1 total tags in treatment: 3354877 INFO @ Tue, 16 Jun 2020 09:55:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:18: #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 09:55:18: #1 tags after filtering in treatment: 3222886 INFO @ Tue, 16 Jun 2020 09:55:18: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 09:55:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:18: #2 number of paired peaks: 324 WARNING @ Tue, 16 Jun 2020 09:55:18: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:18: #2 predicted fragment length is 222 bps INFO @ Tue, 16 Jun 2020 09:55:18: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 16 Jun 2020 09:55:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.05_model.r WARNING @ Tue, 16 Jun 2020 09:55:18: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:18: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Tue, 16 Jun 2020 09:55:18: #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 09:55:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:19: 2000000 INFO @ Tue, 16 Jun 2020 09:55:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:26: 3000000 INFO @ Tue, 16 Jun 2020 09:55:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.05_summits.bed INFO @ Tue, 16 Jun 2020 09:55:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (277 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 09:55:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.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 09:55:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:34: 4000000 INFO @ Tue, 16 Jun 2020 09:55:40: 1000000 INFO @ Tue, 16 Jun 2020 09:55:41: 5000000 INFO @ Tue, 16 Jun 2020 09:55:46: 2000000 INFO @ Tue, 16 Jun 2020 09:55:49: 6000000 INFO @ Tue, 16 Jun 2020 09:55:53: 3000000 INFO @ Tue, 16 Jun 2020 09:55:57: 7000000 INFO @ Tue, 16 Jun 2020 09:55:58: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 09:55:58: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 09:55:58: #1 total tags in treatment: 3354877 INFO @ Tue, 16 Jun 2020 09:55:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:58: #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 09:55:58: #1 tags after filtering in treatment: 3222886 INFO @ Tue, 16 Jun 2020 09:55:58: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 09:55:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:58: #2 number of paired peaks: 324 WARNING @ Tue, 16 Jun 2020 09:55:58: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:58: #2 predicted fragment length is 222 bps INFO @ Tue, 16 Jun 2020 09:55:58: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 16 Jun 2020 09:55:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.10_model.r WARNING @ Tue, 16 Jun 2020 09:55:58: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:58: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Tue, 16 Jun 2020 09:55:58: #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 09:55:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:59: 4000000 INFO @ Tue, 16 Jun 2020 09:56:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:06: 5000000 INFO @ Tue, 16 Jun 2020 09:56:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.10_summits.bed INFO @ Tue, 16 Jun 2020 09:56:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:56:12: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:56:18: 7000000 INFO @ Tue, 16 Jun 2020 09:56:19: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 09:56:19: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 09:56:19: #1 total tags in treatment: 3354877 INFO @ Tue, 16 Jun 2020 09:56:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:19: #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 09:56:19: #1 tags after filtering in treatment: 3222886 INFO @ Tue, 16 Jun 2020 09:56:19: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 09:56:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:19: #2 number of paired peaks: 324 WARNING @ Tue, 16 Jun 2020 09:56:19: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:19: #2 predicted fragment length is 222 bps INFO @ Tue, 16 Jun 2020 09:56:19: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 16 Jun 2020 09:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.20_model.r WARNING @ Tue, 16 Jun 2020 09:56:19: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:19: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Tue, 16 Jun 2020 09:56:19: #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 09:56:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064641/SRX5064641.20_summits.bed INFO @ Tue, 16 Jun 2020 09:56:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (123 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。