Job ID = 8070307 SRX = SRX7217783 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: 00:14:08 8500222 reads; of these: 8500222 (100.00%) were paired; of these: 1178518 (13.86%) aligned concordantly 0 times 6611716 (77.78%) aligned concordantly exactly 1 time 709988 (8.35%) aligned concordantly >1 times ---- 1178518 pairs aligned concordantly 0 times; of these: 317218 (26.92%) aligned discordantly 1 time ---- 861300 pairs aligned 0 times concordantly or discordantly; of these: 1722600 mates make up the pairs; of these: 1519516 (88.21%) aligned 0 times 132978 (7.72%) aligned exactly 1 time 70106 (4.07%) aligned >1 times 91.06% overall alignment rate Time searching: 00:14:08 Overall time: 00:14:08 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] 1598604 / 7603897 = 0.2102 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 13:22:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.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 13:22:51: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:22:51: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:23:00: 1000000 INFO @ Sat, 08 Aug 2020 13:23:09: 2000000 INFO @ Sat, 08 Aug 2020 13:23:17: 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 13:23:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.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 13:23:21: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:23:21: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:23:27: 4000000 INFO @ Sat, 08 Aug 2020 13:23:30: 1000000 INFO @ Sat, 08 Aug 2020 13:23:36: 5000000 INFO @ Sat, 08 Aug 2020 13:23:41: 2000000 INFO @ Sat, 08 Aug 2020 13:23:46: 6000000 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 13:23:51: 3000000 INFO @ Sat, 08 Aug 2020 13:23:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.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 13:23:51: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:23:51: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:23:57: 7000000 INFO @ Sat, 08 Aug 2020 13:24:01: 1000000 INFO @ Sat, 08 Aug 2020 13:24:02: 4000000 INFO @ Sat, 08 Aug 2020 13:24:07: 8000000 INFO @ Sat, 08 Aug 2020 13:24:11: 2000000 INFO @ Sat, 08 Aug 2020 13:24:13: 5000000 INFO @ Sat, 08 Aug 2020 13:24:18: 9000000 INFO @ Sat, 08 Aug 2020 13:24:21: 3000000 INFO @ Sat, 08 Aug 2020 13:24:24: 6000000 INFO @ Sat, 08 Aug 2020 13:24:29: 10000000 INFO @ Sat, 08 Aug 2020 13:24:31: 4000000 INFO @ Sat, 08 Aug 2020 13:24:34: 7000000 INFO @ Sat, 08 Aug 2020 13:24:39: 11000000 INFO @ Sat, 08 Aug 2020 13:24:41: 5000000 INFO @ Sat, 08 Aug 2020 13:24:45: 8000000 INFO @ Sat, 08 Aug 2020 13:24:50: 12000000 INFO @ Sat, 08 Aug 2020 13:24:51: 6000000 INFO @ Sat, 08 Aug 2020 13:24:53: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:24:53: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:24:53: #1 total tags in treatment: 5759778 INFO @ Sat, 08 Aug 2020 13:24:53: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:24:53: #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 13:24:53: #1 tags after filtering in treatment: 5201505 INFO @ Sat, 08 Aug 2020 13:24:53: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:24:53: #1 finished! INFO @ Sat, 08 Aug 2020 13:24:53: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:24:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:24:53: #2 number of paired peaks: 1432 INFO @ Sat, 08 Aug 2020 13:24:53: start model_add_line... INFO @ Sat, 08 Aug 2020 13:24:53: start X-correlation... INFO @ Sat, 08 Aug 2020 13:24:53: end of X-cor INFO @ Sat, 08 Aug 2020 13:24:53: #2 finished! INFO @ Sat, 08 Aug 2020 13:24:53: #2 predicted fragment length is 231 bps INFO @ Sat, 08 Aug 2020 13:24:53: #2 alternative fragment length(s) may be 231 bps INFO @ Sat, 08 Aug 2020 13:24:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.05_model.r WARNING @ Sat, 08 Aug 2020 13:24:53: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:24:53: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Sat, 08 Aug 2020 13:24:53: #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 13:24:53: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:24:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:24:56: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:25:01: 7000000 INFO @ Sat, 08 Aug 2020 13:25:05: 10000000 INFO @ Sat, 08 Aug 2020 13:25:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:25:11: 8000000 INFO @ Sat, 08 Aug 2020 13:25:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:25:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.05_summits.bed INFO @ Sat, 08 Aug 2020 13:25:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5130 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:25:15: 11000000 INFO @ Sat, 08 Aug 2020 13:25:20: 9000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:25:23: 12000000 INFO @ Sat, 08 Aug 2020 13:25:26: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:25:26: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:25:26: #1 total tags in treatment: 5759778 INFO @ Sat, 08 Aug 2020 13:25:26: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:25:26: #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 13:25:26: #1 tags after filtering in treatment: 5201505 INFO @ Sat, 08 Aug 2020 13:25:26: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:25:26: #1 finished! INFO @ Sat, 08 Aug 2020 13:25:26: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:25:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:25:26: #2 number of paired peaks: 1432 INFO @ Sat, 08 Aug 2020 13:25:26: start model_add_line... INFO @ Sat, 08 Aug 2020 13:25:26: start X-correlation... INFO @ Sat, 08 Aug 2020 13:25:27: end of X-cor INFO @ Sat, 08 Aug 2020 13:25:27: #2 finished! INFO @ Sat, 08 Aug 2020 13:25:27: #2 predicted fragment length is 231 bps INFO @ Sat, 08 Aug 2020 13:25:27: #2 alternative fragment length(s) may be 231 bps INFO @ Sat, 08 Aug 2020 13:25:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.10_model.r WARNING @ Sat, 08 Aug 2020 13:25:27: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:25:27: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Sat, 08 Aug 2020 13:25:27: #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 13:25:27: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:25:31: 10000000 INFO @ Sat, 08 Aug 2020 13:25:40: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:25:40: 11000000 INFO @ Sat, 08 Aug 2020 13:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:25:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:25:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.10_summits.bed INFO @ Sat, 08 Aug 2020 13:25:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2985 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:25:50: 12000000 INFO @ Sat, 08 Aug 2020 13:25:52: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:25:52: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:25:52: #1 total tags in treatment: 5759778 INFO @ Sat, 08 Aug 2020 13:25:52: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:25:52: #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 13:25:52: #1 tags after filtering in treatment: 5201505 INFO @ Sat, 08 Aug 2020 13:25:52: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:25:52: #1 finished! INFO @ Sat, 08 Aug 2020 13:25:52: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:25:53: #2 number of paired peaks: 1432 INFO @ Sat, 08 Aug 2020 13:25:53: start model_add_line... INFO @ Sat, 08 Aug 2020 13:25:53: start X-correlation... INFO @ Sat, 08 Aug 2020 13:25:53: end of X-cor INFO @ Sat, 08 Aug 2020 13:25:53: #2 finished! INFO @ Sat, 08 Aug 2020 13:25:53: #2 predicted fragment length is 231 bps INFO @ Sat, 08 Aug 2020 13:25:53: #2 alternative fragment length(s) may be 231 bps INFO @ Sat, 08 Aug 2020 13:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.20_model.r WARNING @ Sat, 08 Aug 2020 13:25:53: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:25:53: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Sat, 08 Aug 2020 13:25:53: #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 13:25:53: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:05: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217783/SRX7217783.20_summits.bed INFO @ Sat, 08 Aug 2020 13:26:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1358 records, 4 fields): 3 millis CompletedMACS2peakCalling