Job ID = 8069379 SRX = SRX7217784 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:31:45 prefetch.2.10.7: 1) Downloading 'SRR10533861'... 2020-08-08T03:31:45 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:33:41 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:33:41 prefetch.2.10.7: 1) 'SRR10533861' was downloaded successfully 2020-08-08T03:33:41 prefetch.2.10.7: 'SRR10533861' has 0 unresolved dependencies Read 8765041 spots for SRR10533861/SRR10533861.sra Written 8765041 spots for SRR10533861/SRR10533861.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070299 ("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: 00:13:32 8765041 reads; of these: 8765041 (100.00%) were paired; of these: 1665194 (19.00%) aligned concordantly 0 times 6331743 (72.24%) aligned concordantly exactly 1 time 768104 (8.76%) aligned concordantly >1 times ---- 1665194 pairs aligned concordantly 0 times; of these: 535038 (32.13%) aligned discordantly 1 time ---- 1130156 pairs aligned 0 times concordantly or discordantly; of these: 2260312 mates make up the pairs; of these: 2023931 (89.54%) aligned 0 times 132536 (5.86%) aligned exactly 1 time 103845 (4.59%) aligned >1 times 88.45% 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] 1494216 / 7592288 = 0.1968 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 12:54:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.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 12:54:08: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:54:08: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:54:14: 1000000 INFO @ Sat, 08 Aug 2020 12:54:20: 2000000 INFO @ Sat, 08 Aug 2020 12:54:26: 3000000 INFO @ Sat, 08 Aug 2020 12:54:32: 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 12:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.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 12:54:38: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:54:38: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:54:39: 5000000 INFO @ Sat, 08 Aug 2020 12:54:44: 1000000 INFO @ Sat, 08 Aug 2020 12:54:45: 6000000 INFO @ Sat, 08 Aug 2020 12:54:51: 2000000 INFO @ Sat, 08 Aug 2020 12:54:51: 7000000 INFO @ Sat, 08 Aug 2020 12:54:57: 3000000 INFO @ Sat, 08 Aug 2020 12:54:58: 8000000 INFO @ Sat, 08 Aug 2020 12:55:04: 4000000 INFO @ Sat, 08 Aug 2020 12:55:04: 9000000 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 12:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.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 12:55:08: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:55:08: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:55:10: 5000000 INFO @ Sat, 08 Aug 2020 12:55:10: 10000000 INFO @ Sat, 08 Aug 2020 12:55:14: 1000000 INFO @ Sat, 08 Aug 2020 12:55:17: 6000000 INFO @ Sat, 08 Aug 2020 12:55:17: 11000000 INFO @ Sat, 08 Aug 2020 12:55:21: 2000000 INFO @ Sat, 08 Aug 2020 12:55:23: 7000000 INFO @ Sat, 08 Aug 2020 12:55:23: 12000000 INFO @ Sat, 08 Aug 2020 12:55:27: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:55:27: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:55:27: #1 total tags in treatment: 5674364 INFO @ Sat, 08 Aug 2020 12:55:27: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:55:27: #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 12:55:27: #1 tags after filtering in treatment: 5079117 INFO @ Sat, 08 Aug 2020 12:55:27: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:55:27: #1 finished! INFO @ Sat, 08 Aug 2020 12:55:27: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:55:27: #2 number of paired peaks: 1187 INFO @ Sat, 08 Aug 2020 12:55:27: start model_add_line... INFO @ Sat, 08 Aug 2020 12:55:27: start X-correlation... INFO @ Sat, 08 Aug 2020 12:55:27: end of X-cor INFO @ Sat, 08 Aug 2020 12:55:27: #2 finished! INFO @ Sat, 08 Aug 2020 12:55:27: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 12:55:27: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 12:55:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.05_model.r WARNING @ Sat, 08 Aug 2020 12:55:27: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:55:27: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 12:55:27: #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 12:55:27: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:55:28: 3000000 INFO @ Sat, 08 Aug 2020 12:55:30: 8000000 INFO @ Sat, 08 Aug 2020 12:55:34: 4000000 INFO @ Sat, 08 Aug 2020 12:55:36: 9000000 INFO @ Sat, 08 Aug 2020 12:55:39: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:55:41: 5000000 INFO @ Sat, 08 Aug 2020 12:55:42: 10000000 INFO @ Sat, 08 Aug 2020 12:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.05_summits.bed INFO @ Sat, 08 Aug 2020 12:55:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4804 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:55:47: 6000000 INFO @ Sat, 08 Aug 2020 12:55:49: 11000000 INFO @ Sat, 08 Aug 2020 12:55:54: 7000000 INFO @ Sat, 08 Aug 2020 12:55:55: 12000000 INFO @ Sat, 08 Aug 2020 12:55:59: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:55:59: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:55:59: #1 total tags in treatment: 5674364 INFO @ Sat, 08 Aug 2020 12:55:59: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:55:59: #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 12:55:59: #1 tags after filtering in treatment: 5079117 INFO @ Sat, 08 Aug 2020 12:55:59: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:55:59: #1 finished! INFO @ Sat, 08 Aug 2020 12:55:59: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:55:59: #2 number of paired peaks: 1187 INFO @ Sat, 08 Aug 2020 12:55:59: start model_add_line... INFO @ Sat, 08 Aug 2020 12:55:59: start X-correlation... INFO @ Sat, 08 Aug 2020 12:55:59: end of X-cor INFO @ Sat, 08 Aug 2020 12:55:59: #2 finished! INFO @ Sat, 08 Aug 2020 12:55:59: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 12:55:59: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 12:55:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.10_model.r WARNING @ Sat, 08 Aug 2020 12:55:59: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:55:59: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 12:55:59: #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 12:55:59: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:56:00: 8000000 INFO @ Sat, 08 Aug 2020 12:56:06: 9000000 INFO @ Sat, 08 Aug 2020 12:56:11: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:56:13: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:56:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:56:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:56:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.10_summits.bed INFO @ Sat, 08 Aug 2020 12:56:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2818 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:56:19: 11000000 INFO @ Sat, 08 Aug 2020 12:56:25: 12000000 INFO @ Sat, 08 Aug 2020 12:56:29: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:56:29: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:56:29: #1 total tags in treatment: 5674364 INFO @ Sat, 08 Aug 2020 12:56:29: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:56:29: #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 12:56:29: #1 tags after filtering in treatment: 5079117 INFO @ Sat, 08 Aug 2020 12:56:29: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:56:29: #1 finished! INFO @ Sat, 08 Aug 2020 12:56:29: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:56:29: #2 number of paired peaks: 1187 INFO @ Sat, 08 Aug 2020 12:56:29: start model_add_line... INFO @ Sat, 08 Aug 2020 12:56:29: start X-correlation... INFO @ Sat, 08 Aug 2020 12:56:29: end of X-cor INFO @ Sat, 08 Aug 2020 12:56:29: #2 finished! INFO @ Sat, 08 Aug 2020 12:56:29: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 12:56:29: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 12:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.20_model.r WARNING @ Sat, 08 Aug 2020 12:56:29: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:56:29: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 12:56:29: #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 12:56:29: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:56:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:56:40: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:56:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:56:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:56:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217784/SRX7217784.20_summits.bed INFO @ Sat, 08 Aug 2020 12:56:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1247 records, 4 fields): 3 millis CompletedMACS2peakCalling