Job ID = 8070403 SRX = SRX8392418 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: 00:14:21 8304521 reads; of these: 8304521 (100.00%) were paired; of these: 696856 (8.39%) aligned concordantly 0 times 6826900 (82.21%) aligned concordantly exactly 1 time 780765 (9.40%) aligned concordantly >1 times ---- 696856 pairs aligned concordantly 0 times; of these: 302616 (43.43%) aligned discordantly 1 time ---- 394240 pairs aligned 0 times concordantly or discordantly; of these: 788480 mates make up the pairs; of these: 594114 (75.35%) aligned 0 times 119825 (15.20%) aligned exactly 1 time 74541 (9.45%) aligned >1 times 96.42% overall alignment rate Time searching: 00:14:21 Overall time: 00:14:21 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] 1973888 / 7867743 = 0.2509 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 13:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.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 13:25:34: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:34: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:43: 1000000 INFO @ Sat, 08 Aug 2020 13:25:52: 2000000 INFO @ Sat, 08 Aug 2020 13:26:00: 3000000 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 13:26:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.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 13:26:04: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:04: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:10: 4000000 INFO @ Sat, 08 Aug 2020 13:26:13: 1000000 INFO @ Sat, 08 Aug 2020 13:26:19: 5000000 INFO @ Sat, 08 Aug 2020 13:26:21: 2000000 INFO @ Sat, 08 Aug 2020 13:26:29: 6000000 INFO @ Sat, 08 Aug 2020 13:26:30: 3000000 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 13:26:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.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 13:26:34: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:34: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:38: 4000000 INFO @ Sat, 08 Aug 2020 13:26:39: 7000000 INFO @ Sat, 08 Aug 2020 13:26:43: 1000000 INFO @ Sat, 08 Aug 2020 13:26:47: 5000000 INFO @ Sat, 08 Aug 2020 13:26:49: 8000000 INFO @ Sat, 08 Aug 2020 13:26:51: 2000000 INFO @ Sat, 08 Aug 2020 13:26:56: 6000000 INFO @ Sat, 08 Aug 2020 13:26:58: 9000000 INFO @ Sat, 08 Aug 2020 13:27:00: 3000000 INFO @ Sat, 08 Aug 2020 13:27:05: 7000000 INFO @ Sat, 08 Aug 2020 13:27:08: 10000000 INFO @ Sat, 08 Aug 2020 13:27:09: 4000000 INFO @ Sat, 08 Aug 2020 13:27:13: 8000000 INFO @ Sat, 08 Aug 2020 13:27:17: 11000000 INFO @ Sat, 08 Aug 2020 13:27:17: 5000000 INFO @ Sat, 08 Aug 2020 13:27:22: 9000000 INFO @ Sat, 08 Aug 2020 13:27:26: 6000000 INFO @ Sat, 08 Aug 2020 13:27:27: 12000000 INFO @ Sat, 08 Aug 2020 13:27:27: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:27:27: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:27:27: #1 total tags in treatment: 5669565 INFO @ Sat, 08 Aug 2020 13:27:27: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:27: #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 13:27:28: #1 tags after filtering in treatment: 5246549 INFO @ Sat, 08 Aug 2020 13:27:28: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:27:28: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:28: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:28: #2 number of paired peaks: 1117 INFO @ Sat, 08 Aug 2020 13:27:28: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:28: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:28: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:28: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:28: #2 predicted fragment length is 226 bps INFO @ Sat, 08 Aug 2020 13:27:28: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 08 Aug 2020 13:27:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.05_model.r WARNING @ Sat, 08 Aug 2020 13:27:28: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:27:28: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Sat, 08 Aug 2020 13:27:28: #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 13:27:28: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:31: 10000000 INFO @ Sat, 08 Aug 2020 13:27:35: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:27:39: 11000000 INFO @ Sat, 08 Aug 2020 13:27:40: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:43: 8000000 INFO @ Sat, 08 Aug 2020 13:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.05_summits.bed INFO @ Sat, 08 Aug 2020 13:27:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6398 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:27:48: 12000000 INFO @ Sat, 08 Aug 2020 13:27:48: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:27:48: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:27:48: #1 total tags in treatment: 5669565 INFO @ Sat, 08 Aug 2020 13:27:48: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:48: #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 13:27:48: #1 tags after filtering in treatment: 5246549 INFO @ Sat, 08 Aug 2020 13:27:48: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:27:48: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:48: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:49: #2 number of paired peaks: 1117 INFO @ Sat, 08 Aug 2020 13:27:49: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:49: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:49: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:49: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:49: #2 predicted fragment length is 226 bps INFO @ Sat, 08 Aug 2020 13:27:49: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 08 Aug 2020 13:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.10_model.r WARNING @ Sat, 08 Aug 2020 13:27:49: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:27:49: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Sat, 08 Aug 2020 13:27:49: #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 13:27:49: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:51: 9000000 INFO @ Sat, 08 Aug 2020 13:27:59: 10000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:28:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.10_summits.bed INFO @ Sat, 08 Aug 2020 13:28:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3605 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:28:06: 11000000 INFO @ Sat, 08 Aug 2020 13:28:13: 12000000 INFO @ Sat, 08 Aug 2020 13:28:14: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:14: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:14: #1 total tags in treatment: 5669565 INFO @ Sat, 08 Aug 2020 13:28:14: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:14: #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 13:28:14: #1 tags after filtering in treatment: 5246549 INFO @ Sat, 08 Aug 2020 13:28:14: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:28:14: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:14: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:14: #2 number of paired peaks: 1117 INFO @ Sat, 08 Aug 2020 13:28:14: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:14: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:14: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:14: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:14: #2 predicted fragment length is 226 bps INFO @ Sat, 08 Aug 2020 13:28:14: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 08 Aug 2020 13:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.20_model.r WARNING @ Sat, 08 Aug 2020 13:28:14: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:14: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Sat, 08 Aug 2020 13:28:14: #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 13:28:14: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:28:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392418/SRX8392418.20_summits.bed INFO @ Sat, 08 Aug 2020 13:28:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1384 records, 4 fields): 3 millis CompletedMACS2peakCalling