Job ID = 8070689 SRX = SRX7217793 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: 00:17:32 9509995 reads; of these: 9509995 (100.00%) were paired; of these: 797383 (8.38%) aligned concordantly 0 times 7868438 (82.74%) aligned concordantly exactly 1 time 844174 (8.88%) aligned concordantly >1 times ---- 797383 pairs aligned concordantly 0 times; of these: 372745 (46.75%) aligned discordantly 1 time ---- 424638 pairs aligned 0 times concordantly or discordantly; of these: 849276 mates make up the pairs; of these: 634345 (74.69%) aligned 0 times 125491 (14.78%) aligned exactly 1 time 89440 (10.53%) aligned >1 times 96.66% overall alignment rate Time searching: 00:17:32 Overall time: 00:17:32 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 16 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] 2532396 / 9049164 = 0.2798 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 13:32:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.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 13:32:58: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:32:58: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:33:05: 1000000 INFO @ Sat, 08 Aug 2020 13:33:12: 2000000 INFO @ Sat, 08 Aug 2020 13:33:20: 3000000 INFO @ Sat, 08 Aug 2020 13:33:26: 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 13:33:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.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 13:33:28: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:33:28: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:33:33: 5000000 INFO @ Sat, 08 Aug 2020 13:33:35: 1000000 INFO @ Sat, 08 Aug 2020 13:33:40: 6000000 INFO @ Sat, 08 Aug 2020 13:33:43: 2000000 INFO @ Sat, 08 Aug 2020 13:33:48: 7000000 INFO @ Sat, 08 Aug 2020 13:33:50: 3000000 INFO @ Sat, 08 Aug 2020 13:33:56: 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 13:33:58: 4000000 INFO @ Sat, 08 Aug 2020 13:33:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.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 13:33:58: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:33:58: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:34:04: 9000000 INFO @ Sat, 08 Aug 2020 13:34:06: 5000000 INFO @ Sat, 08 Aug 2020 13:34:06: 1000000 INFO @ Sat, 08 Aug 2020 13:34:12: 10000000 INFO @ Sat, 08 Aug 2020 13:34:14: 6000000 INFO @ Sat, 08 Aug 2020 13:34:14: 2000000 INFO @ Sat, 08 Aug 2020 13:34:20: 11000000 INFO @ Sat, 08 Aug 2020 13:34:21: 7000000 INFO @ Sat, 08 Aug 2020 13:34:22: 3000000 INFO @ Sat, 08 Aug 2020 13:34:28: 12000000 INFO @ Sat, 08 Aug 2020 13:34:29: 8000000 INFO @ Sat, 08 Aug 2020 13:34:30: 4000000 INFO @ Sat, 08 Aug 2020 13:34:36: 13000000 INFO @ Sat, 08 Aug 2020 13:34:37: 9000000 INFO @ Sat, 08 Aug 2020 13:34:38: 5000000 INFO @ Sat, 08 Aug 2020 13:34:39: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:34:39: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:34:39: #1 total tags in treatment: 6231334 INFO @ Sat, 08 Aug 2020 13:34:39: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:34:39: #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 13:34:39: #1 tags after filtering in treatment: 5568717 INFO @ Sat, 08 Aug 2020 13:34:39: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 13:34:39: #1 finished! INFO @ Sat, 08 Aug 2020 13:34:39: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:34:39: #2 number of paired peaks: 2990 INFO @ Sat, 08 Aug 2020 13:34:39: start model_add_line... INFO @ Sat, 08 Aug 2020 13:34:39: start X-correlation... INFO @ Sat, 08 Aug 2020 13:34:39: end of X-cor INFO @ Sat, 08 Aug 2020 13:34:39: #2 finished! INFO @ Sat, 08 Aug 2020 13:34:39: #2 predicted fragment length is 243 bps INFO @ Sat, 08 Aug 2020 13:34:39: #2 alternative fragment length(s) may be 243 bps INFO @ Sat, 08 Aug 2020 13:34:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.05_model.r WARNING @ Sat, 08 Aug 2020 13:34:39: #2 Since the d (243) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:34:39: #2 You may need to consider one of the other alternative d(s): 243 WARNING @ Sat, 08 Aug 2020 13:34:39: #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 13:34:39: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:34:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:34:44: 10000000 INFO @ Sat, 08 Aug 2020 13:34:46: 6000000 INFO @ Sat, 08 Aug 2020 13:34:52: 11000000 INFO @ Sat, 08 Aug 2020 13:34:54: 7000000 INFO @ Sat, 08 Aug 2020 13:34:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:34:59: 12000000 INFO @ Sat, 08 Aug 2020 13:35:01: 8000000 INFO @ Sat, 08 Aug 2020 13:35:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:35:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:35:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.05_summits.bed INFO @ Sat, 08 Aug 2020 13:35:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8249 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:35:07: 13000000 INFO @ Sat, 08 Aug 2020 13:35:09: 9000000 INFO @ Sat, 08 Aug 2020 13:35:09: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:35:09: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:35:09: #1 total tags in treatment: 6231334 INFO @ Sat, 08 Aug 2020 13:35:09: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:35:09: #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 13:35:09: #1 tags after filtering in treatment: 5568717 INFO @ Sat, 08 Aug 2020 13:35:09: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 13:35:09: #1 finished! INFO @ Sat, 08 Aug 2020 13:35:09: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:35:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:35:10: #2 number of paired peaks: 2990 INFO @ Sat, 08 Aug 2020 13:35:10: start model_add_line... INFO @ Sat, 08 Aug 2020 13:35:10: start X-correlation... INFO @ Sat, 08 Aug 2020 13:35:10: end of X-cor INFO @ Sat, 08 Aug 2020 13:35:10: #2 finished! INFO @ Sat, 08 Aug 2020 13:35:10: #2 predicted fragment length is 243 bps INFO @ Sat, 08 Aug 2020 13:35:10: #2 alternative fragment length(s) may be 243 bps INFO @ Sat, 08 Aug 2020 13:35:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.10_model.r WARNING @ Sat, 08 Aug 2020 13:35:10: #2 Since the d (243) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:35:10: #2 You may need to consider one of the other alternative d(s): 243 WARNING @ Sat, 08 Aug 2020 13:35:10: #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 13:35:10: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:35:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:35:16: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:35:23: 11000000 INFO @ Sat, 08 Aug 2020 13:35:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:35:31: 12000000 INFO @ Sat, 08 Aug 2020 13:35:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:35:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:35:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.10_summits.bed INFO @ Sat, 08 Aug 2020 13:35:36: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6171 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:35:38: 13000000 INFO @ Sat, 08 Aug 2020 13:35:40: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:35:40: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:35:40: #1 total tags in treatment: 6231334 INFO @ Sat, 08 Aug 2020 13:35:40: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:35:40: #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 13:35:40: #1 tags after filtering in treatment: 5568717 INFO @ Sat, 08 Aug 2020 13:35:40: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 13:35:40: #1 finished! INFO @ Sat, 08 Aug 2020 13:35:40: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:35:40: #2 number of paired peaks: 2990 INFO @ Sat, 08 Aug 2020 13:35:40: start model_add_line... INFO @ Sat, 08 Aug 2020 13:35:41: start X-correlation... INFO @ Sat, 08 Aug 2020 13:35:41: end of X-cor INFO @ Sat, 08 Aug 2020 13:35:41: #2 finished! INFO @ Sat, 08 Aug 2020 13:35:41: #2 predicted fragment length is 243 bps INFO @ Sat, 08 Aug 2020 13:35:41: #2 alternative fragment length(s) may be 243 bps INFO @ Sat, 08 Aug 2020 13:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.20_model.r WARNING @ Sat, 08 Aug 2020 13:35:41: #2 Since the d (243) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:35:41: #2 You may need to consider one of the other alternative d(s): 243 WARNING @ Sat, 08 Aug 2020 13:35:41: #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 13:35:41: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:35:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:35:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:36:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:36:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:36:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217793/SRX7217793.20_summits.bed INFO @ Sat, 08 Aug 2020 13:36:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3536 records, 4 fields): 5 millis CompletedMACS2peakCalling