Job ID = 8070461 SRX = SRX7217791 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:13:32 7395069 reads; of these: 7395069 (100.00%) were paired; of these: 807258 (10.92%) aligned concordantly 0 times 5780951 (78.17%) aligned concordantly exactly 1 time 806860 (10.91%) aligned concordantly >1 times ---- 807258 pairs aligned concordantly 0 times; of these: 290120 (35.94%) aligned discordantly 1 time ---- 517138 pairs aligned 0 times concordantly or discordantly; of these: 1034276 mates make up the pairs; of these: 851382 (82.32%) aligned 0 times 99614 (9.63%) aligned exactly 1 time 83280 (8.05%) aligned >1 times 94.24% overall alignment rate Time searching: 00:13:32 Overall time: 00:13:32 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] 2614491 / 6854544 = 0.3814 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 13:24:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.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 13:24:57: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:24:57: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:04: 1000000 INFO @ Sat, 08 Aug 2020 13:25:11: 2000000 INFO @ Sat, 08 Aug 2020 13:25:17: 3000000 INFO @ Sat, 08 Aug 2020 13:25:24: 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 13:25:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.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 13:25:27: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:27: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:31: 5000000 INFO @ Sat, 08 Aug 2020 13:25:34: 1000000 INFO @ Sat, 08 Aug 2020 13:25:38: 6000000 INFO @ Sat, 08 Aug 2020 13:25:42: 2000000 INFO @ Sat, 08 Aug 2020 13:25:46: 7000000 INFO @ Sat, 08 Aug 2020 13:25:49: 3000000 INFO @ Sat, 08 Aug 2020 13:25:53: 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 13:25:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.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 13:25:57: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:57: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:57: 4000000 INFO @ Sat, 08 Aug 2020 13:25:59: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:25:59: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:25:59: #1 total tags in treatment: 4020907 INFO @ Sat, 08 Aug 2020 13:25:59: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:25:59: #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 13:25:59: #1 tags after filtering in treatment: 3615859 INFO @ Sat, 08 Aug 2020 13:25:59: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:25:59: #1 finished! INFO @ Sat, 08 Aug 2020 13:25:59: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:25:59: #2 number of paired peaks: 1756 INFO @ Sat, 08 Aug 2020 13:25:59: start model_add_line... INFO @ Sat, 08 Aug 2020 13:25:59: start X-correlation... INFO @ Sat, 08 Aug 2020 13:25:59: end of X-cor INFO @ Sat, 08 Aug 2020 13:25:59: #2 finished! INFO @ Sat, 08 Aug 2020 13:25:59: #2 predicted fragment length is 219 bps INFO @ Sat, 08 Aug 2020 13:25:59: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 08 Aug 2020 13:25:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.05_model.r WARNING @ Sat, 08 Aug 2020 13:25:59: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:25:59: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Sat, 08 Aug 2020 13:25:59: #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 13:25:59: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:04: 5000000 INFO @ Sat, 08 Aug 2020 13:26:05: 1000000 INFO @ Sat, 08 Aug 2020 13:26:08: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:12: 6000000 INFO @ Sat, 08 Aug 2020 13:26:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.05_summits.bed INFO @ Sat, 08 Aug 2020 13:26:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4571 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:26:14: 2000000 INFO @ Sat, 08 Aug 2020 13:26:19: 7000000 INFO @ Sat, 08 Aug 2020 13:26:22: 3000000 INFO @ Sat, 08 Aug 2020 13:26:27: 8000000 INFO @ Sat, 08 Aug 2020 13:26:31: 4000000 INFO @ Sat, 08 Aug 2020 13:26:32: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:26:32: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:26:32: #1 total tags in treatment: 4020907 INFO @ Sat, 08 Aug 2020 13:26:32: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:32: #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 13:26:32: #1 tags after filtering in treatment: 3615859 INFO @ Sat, 08 Aug 2020 13:26:32: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:26:32: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:32: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:32: #2 number of paired peaks: 1756 INFO @ Sat, 08 Aug 2020 13:26:32: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:32: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:32: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:32: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:32: #2 predicted fragment length is 219 bps INFO @ Sat, 08 Aug 2020 13:26:32: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 08 Aug 2020 13:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.10_model.r WARNING @ Sat, 08 Aug 2020 13:26:32: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:26:32: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Sat, 08 Aug 2020 13:26:32: #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 13:26:32: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:40: 5000000 INFO @ Sat, 08 Aug 2020 13:26:41: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.10_summits.bed INFO @ Sat, 08 Aug 2020 13:26:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2321 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:26:48: 6000000 INFO @ Sat, 08 Aug 2020 13:26:56: 7000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:27:05: 8000000 INFO @ Sat, 08 Aug 2020 13:27:10: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:27:10: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:27:10: #1 total tags in treatment: 4020907 INFO @ Sat, 08 Aug 2020 13:27:10: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:10: #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 13:27:10: #1 tags after filtering in treatment: 3615859 INFO @ Sat, 08 Aug 2020 13:27:10: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:27:10: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:10: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:11: #2 number of paired peaks: 1756 INFO @ Sat, 08 Aug 2020 13:27:11: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:11: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:11: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:11: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:11: #2 predicted fragment length is 219 bps INFO @ Sat, 08 Aug 2020 13:27:11: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 08 Aug 2020 13:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.20_model.r WARNING @ Sat, 08 Aug 2020 13:27:11: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:27:11: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Sat, 08 Aug 2020 13:27:11: #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 13:27:11: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:19: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217791/SRX7217791.20_summits.bed INFO @ Sat, 08 Aug 2020 13:27:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (894 records, 4 fields): 15 millis CompletedMACS2peakCalling