Job ID = 8069416 SRX = SRX8392415 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:30 prefetch.2.10.7: 1) Downloading 'SRR11842068'... 2020-08-08T03:32:31 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:57 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:57 prefetch.2.10.7: 1) 'SRR11842068' was downloaded successfully 2020-08-08T03:34:57 prefetch.2.10.7: 'SRR11842068' has 0 unresolved dependencies Read 8227270 spots for SRR11842068/SRR11842068.sra Written 8227270 spots for SRR11842068/SRR11842068.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070411 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:33 8227270 reads; of these: 8227270 (100.00%) were paired; of these: 2231323 (27.12%) aligned concordantly 0 times 5116916 (62.19%) aligned concordantly exactly 1 time 879031 (10.68%) aligned concordantly >1 times ---- 2231323 pairs aligned concordantly 0 times; of these: 917715 (41.13%) aligned discordantly 1 time ---- 1313608 pairs aligned 0 times concordantly or discordantly; of these: 2627216 mates make up the pairs; of these: 2319513 (88.29%) aligned 0 times 137791 (5.24%) aligned exactly 1 time 169912 (6.47%) aligned >1 times 85.90% overall alignment rate Time searching: 00:14:33 Overall time: 00:14:33 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 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] 1050818 / 6858874 = 0.1532 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 12:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.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 12:56:13: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:13: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:20: 1000000 INFO @ Sat, 08 Aug 2020 12:56:26: 2000000 INFO @ Sat, 08 Aug 2020 12:56:33: 3000000 INFO @ Sat, 08 Aug 2020 12:56:40: 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 @ Sat, 08 Aug 2020 12:56:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.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 12:56:43: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:43: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:47: 5000000 INFO @ Sat, 08 Aug 2020 12:56:50: 1000000 INFO @ Sat, 08 Aug 2020 12:56:54: 6000000 INFO @ Sat, 08 Aug 2020 12:56:57: 2000000 INFO @ Sat, 08 Aug 2020 12:57:01: 7000000 INFO @ Sat, 08 Aug 2020 12:57:04: 3000000 INFO @ Sat, 08 Aug 2020 12:57:08: 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 @ Sat, 08 Aug 2020 12:57:11: 4000000 INFO @ Sat, 08 Aug 2020 12:57:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.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 12:57:13: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:13: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:16: 9000000 INFO @ Sat, 08 Aug 2020 12:57:18: 5000000 INFO @ Sat, 08 Aug 2020 12:57:22: 1000000 INFO @ Sat, 08 Aug 2020 12:57:23: 10000000 INFO @ Sat, 08 Aug 2020 12:57:26: 6000000 INFO @ Sat, 08 Aug 2020 12:57:31: 11000000 INFO @ Sat, 08 Aug 2020 12:57:31: 2000000 INFO @ Sat, 08 Aug 2020 12:57:33: 7000000 INFO @ Sat, 08 Aug 2020 12:57:38: 12000000 INFO @ Sat, 08 Aug 2020 12:57:39: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:57:39: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:57:39: #1 total tags in treatment: 5057379 INFO @ Sat, 08 Aug 2020 12:57:39: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:57:39: #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 12:57:39: #1 tags after filtering in treatment: 4708153 INFO @ Sat, 08 Aug 2020 12:57:39: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:57:39: #1 finished! INFO @ Sat, 08 Aug 2020 12:57:39: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:57:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:57:39: #2 number of paired peaks: 451 WARNING @ Sat, 08 Aug 2020 12:57:39: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sat, 08 Aug 2020 12:57:39: start model_add_line... INFO @ Sat, 08 Aug 2020 12:57:39: start X-correlation... INFO @ Sat, 08 Aug 2020 12:57:39: end of X-cor INFO @ Sat, 08 Aug 2020 12:57:39: #2 finished! INFO @ Sat, 08 Aug 2020 12:57:39: #2 predicted fragment length is 198 bps INFO @ Sat, 08 Aug 2020 12:57:39: #2 alternative fragment length(s) may be 198 bps INFO @ Sat, 08 Aug 2020 12:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.05_model.r WARNING @ Sat, 08 Aug 2020 12:57:39: #2 Since the d (198) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:57:39: #2 You may need to consider one of the other alternative d(s): 198 WARNING @ Sat, 08 Aug 2020 12:57:39: #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 12:57:39: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:57:40: 3000000 INFO @ Sat, 08 Aug 2020 12:57:41: 8000000 INFO @ Sat, 08 Aug 2020 12:57:48: 9000000 INFO @ Sat, 08 Aug 2020 12:57:49: 4000000 INFO @ Sat, 08 Aug 2020 12:57:50: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:57:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:57:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:57:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.05_summits.bed INFO @ Sat, 08 Aug 2020 12:57:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (346 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:57:56: 10000000 INFO @ Sat, 08 Aug 2020 12:57:59: 5000000 INFO @ Sat, 08 Aug 2020 12:58:03: 11000000 INFO @ Sat, 08 Aug 2020 12:58:07: 6000000 INFO @ Sat, 08 Aug 2020 12:58:11: 12000000 INFO @ Sat, 08 Aug 2020 12:58:11: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:11: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:11: #1 total tags in treatment: 5057379 INFO @ Sat, 08 Aug 2020 12:58:11: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:11: #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 12:58:11: #1 tags after filtering in treatment: 4708153 INFO @ Sat, 08 Aug 2020 12:58:11: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:58:11: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:11: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:11: #2 number of paired peaks: 451 WARNING @ Sat, 08 Aug 2020 12:58:11: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:11: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:11: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:11: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:11: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:11: #2 predicted fragment length is 198 bps INFO @ Sat, 08 Aug 2020 12:58:11: #2 alternative fragment length(s) may be 198 bps INFO @ Sat, 08 Aug 2020 12:58:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.10_model.r WARNING @ Sat, 08 Aug 2020 12:58:11: #2 Since the d (198) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:11: #2 You may need to consider one of the other alternative d(s): 198 WARNING @ Sat, 08 Aug 2020 12:58:11: #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 12:58:11: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:16: 7000000 INFO @ Sat, 08 Aug 2020 12:58:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:58:25: 8000000 INFO @ Sat, 08 Aug 2020 12:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.10_summits.bed INFO @ Sat, 08 Aug 2020 12:58:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (245 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:34: 9000000 INFO @ Sat, 08 Aug 2020 12:58:43: 10000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:58:52: 11000000 INFO @ Sat, 08 Aug 2020 12:59:01: 12000000 INFO @ Sat, 08 Aug 2020 12:59:01: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:01: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:01: #1 total tags in treatment: 5057379 INFO @ Sat, 08 Aug 2020 12:59:01: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:01: #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 12:59:01: #1 tags after filtering in treatment: 4708153 INFO @ Sat, 08 Aug 2020 12:59:01: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:59:01: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:01: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:01: #2 number of paired peaks: 451 WARNING @ Sat, 08 Aug 2020 12:59:01: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sat, 08 Aug 2020 12:59:01: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:01: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:01: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:01: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:01: #2 predicted fragment length is 198 bps INFO @ Sat, 08 Aug 2020 12:59:01: #2 alternative fragment length(s) may be 198 bps INFO @ Sat, 08 Aug 2020 12:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.20_model.r WARNING @ Sat, 08 Aug 2020 12:59:01: #2 Since the d (198) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:01: #2 You may need to consider one of the other alternative d(s): 198 WARNING @ Sat, 08 Aug 2020 12:59:01: #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 12:59:01: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:12: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392415/SRX8392415.20_summits.bed INFO @ Sat, 08 Aug 2020 12:59:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (186 records, 4 fields): 1 millis CompletedMACS2peakCalling