Job ID = 8070555 SRX = SRX7217792 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: 00:15:16 8412168 reads; of these: 8412168 (100.00%) were paired; of these: 997886 (11.86%) aligned concordantly 0 times 6550367 (77.87%) aligned concordantly exactly 1 time 863915 (10.27%) aligned concordantly >1 times ---- 997886 pairs aligned concordantly 0 times; of these: 416058 (41.69%) aligned discordantly 1 time ---- 581828 pairs aligned 0 times concordantly or discordantly; of these: 1163656 mates make up the pairs; of these: 953879 (81.97%) aligned 0 times 109554 (9.41%) aligned exactly 1 time 100223 (8.61%) aligned >1 times 94.33% overall alignment rate Time searching: 00:15:16 Overall time: 00:15:16 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] 2167491 / 7796948 = 0.2780 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 13:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.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 13:28:35: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:28:35: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:28:41: 1000000 INFO @ Sat, 08 Aug 2020 13:28:48: 2000000 INFO @ Sat, 08 Aug 2020 13:28:54: 3000000 INFO @ Sat, 08 Aug 2020 13:29:01: 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 13:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.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 13:29:05: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:29:05: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:29:07: 5000000 INFO @ Sat, 08 Aug 2020 13:29:11: 1000000 INFO @ Sat, 08 Aug 2020 13:29:13: 6000000 INFO @ Sat, 08 Aug 2020 13:29:17: 2000000 INFO @ Sat, 08 Aug 2020 13:29:19: 7000000 INFO @ Sat, 08 Aug 2020 13:29:23: 3000000 INFO @ Sat, 08 Aug 2020 13:29:25: 8000000 INFO @ Sat, 08 Aug 2020 13:29:29: 4000000 INFO @ Sat, 08 Aug 2020 13:29:31: 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 13:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.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 13:29:35: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:29:35: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:29:35: 5000000 INFO @ Sat, 08 Aug 2020 13:29:38: 10000000 INFO @ Sat, 08 Aug 2020 13:29:41: 6000000 INFO @ Sat, 08 Aug 2020 13:29:42: 1000000 INFO @ Sat, 08 Aug 2020 13:29:44: 11000000 INFO @ Sat, 08 Aug 2020 13:29:47: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:29:47: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:29:47: #1 total tags in treatment: 5303372 INFO @ Sat, 08 Aug 2020 13:29:47: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:29:47: #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 13:29:47: #1 tags after filtering in treatment: 4784196 INFO @ Sat, 08 Aug 2020 13:29:47: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:29:47: #1 finished! INFO @ Sat, 08 Aug 2020 13:29:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:29:47: 7000000 INFO @ Sat, 08 Aug 2020 13:29:48: #2 number of paired peaks: 1236 INFO @ Sat, 08 Aug 2020 13:29:48: start model_add_line... INFO @ Sat, 08 Aug 2020 13:29:48: start X-correlation... INFO @ Sat, 08 Aug 2020 13:29:48: end of X-cor INFO @ Sat, 08 Aug 2020 13:29:48: #2 finished! INFO @ Sat, 08 Aug 2020 13:29:48: #2 predicted fragment length is 218 bps INFO @ Sat, 08 Aug 2020 13:29:48: #2 alternative fragment length(s) may be 218 bps INFO @ Sat, 08 Aug 2020 13:29:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.05_model.r WARNING @ Sat, 08 Aug 2020 13:29:48: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:29:48: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Sat, 08 Aug 2020 13:29:48: #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 13:29:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:29:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:29:50: 2000000 INFO @ Sat, 08 Aug 2020 13:29:54: 8000000 INFO @ Sat, 08 Aug 2020 13:29:57: 3000000 INFO @ Sat, 08 Aug 2020 13:30:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:30:00: 9000000 INFO @ Sat, 08 Aug 2020 13:30:04: 4000000 INFO @ Sat, 08 Aug 2020 13:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.05_summits.bed INFO @ Sat, 08 Aug 2020 13:30:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5388 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:30:06: 10000000 INFO @ Sat, 08 Aug 2020 13:30:12: 5000000 INFO @ Sat, 08 Aug 2020 13:30:12: 11000000 INFO @ Sat, 08 Aug 2020 13:30:16: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:30:16: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:30:16: #1 total tags in treatment: 5303372 INFO @ Sat, 08 Aug 2020 13:30:16: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:30:16: #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 13:30:16: #1 tags after filtering in treatment: 4784196 INFO @ Sat, 08 Aug 2020 13:30:16: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:30:16: #1 finished! INFO @ Sat, 08 Aug 2020 13:30:16: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:30:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:30:16: #2 number of paired peaks: 1236 INFO @ Sat, 08 Aug 2020 13:30:16: start model_add_line... INFO @ Sat, 08 Aug 2020 13:30:16: start X-correlation... INFO @ Sat, 08 Aug 2020 13:30:16: end of X-cor INFO @ Sat, 08 Aug 2020 13:30:16: #2 finished! INFO @ Sat, 08 Aug 2020 13:30:16: #2 predicted fragment length is 218 bps INFO @ Sat, 08 Aug 2020 13:30:16: #2 alternative fragment length(s) may be 218 bps INFO @ Sat, 08 Aug 2020 13:30:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.10_model.r WARNING @ Sat, 08 Aug 2020 13:30:16: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:30:16: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Sat, 08 Aug 2020 13:30:16: #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 13:30:16: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:30:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:30:19: 6000000 INFO @ Sat, 08 Aug 2020 13:30:26: 7000000 INFO @ Sat, 08 Aug 2020 13:30:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:30:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:30:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:30:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.10_summits.bed INFO @ Sat, 08 Aug 2020 13:30:33: Done! INFO @ Sat, 08 Aug 2020 13:30:33: 8000000 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2967 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:30:40: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:30:47: 10000000 INFO @ Sat, 08 Aug 2020 13:30:55: 11000000 INFO @ Sat, 08 Aug 2020 13:30:59: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:30:59: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:30:59: #1 total tags in treatment: 5303372 INFO @ Sat, 08 Aug 2020 13:30:59: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:30:59: #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 13:30:59: #1 tags after filtering in treatment: 4784196 INFO @ Sat, 08 Aug 2020 13:30:59: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:30:59: #1 finished! INFO @ Sat, 08 Aug 2020 13:30:59: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:30:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:30:59: #2 number of paired peaks: 1236 INFO @ Sat, 08 Aug 2020 13:30:59: start model_add_line... INFO @ Sat, 08 Aug 2020 13:30:59: start X-correlation... INFO @ Sat, 08 Aug 2020 13:30:59: end of X-cor INFO @ Sat, 08 Aug 2020 13:30:59: #2 finished! INFO @ Sat, 08 Aug 2020 13:30:59: #2 predicted fragment length is 218 bps INFO @ Sat, 08 Aug 2020 13:30:59: #2 alternative fragment length(s) may be 218 bps INFO @ Sat, 08 Aug 2020 13:30:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.20_model.r WARNING @ Sat, 08 Aug 2020 13:30:59: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:30:59: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Sat, 08 Aug 2020 13:30:59: #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 13:30:59: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:30:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:31:10: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:31:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:31:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:31:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217792/SRX7217792.20_summits.bed INFO @ Sat, 08 Aug 2020 13:31:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1144 records, 4 fields): 3 millis CompletedMACS2peakCalling