Job ID = 8070435 SRX = SRX8392420 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: 00:14:19 8332701 reads; of these: 8332701 (100.00%) were paired; of these: 740007 (8.88%) aligned concordantly 0 times 6939252 (83.28%) aligned concordantly exactly 1 time 653442 (7.84%) aligned concordantly >1 times ---- 740007 pairs aligned concordantly 0 times; of these: 308831 (41.73%) aligned discordantly 1 time ---- 431176 pairs aligned 0 times concordantly or discordantly; of these: 862352 mates make up the pairs; of these: 687936 (79.77%) aligned 0 times 107961 (12.52%) aligned exactly 1 time 66455 (7.71%) aligned >1 times 95.87% overall alignment rate Time searching: 00:14:19 Overall time: 00:14:19 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] 1759353 / 7859808 = 0.2238 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 13:26:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.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 13:26:36: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:36: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:44: 1000000 INFO @ Sat, 08 Aug 2020 13:26:52: 2000000 INFO @ Sat, 08 Aug 2020 13:27:00: 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 13:27:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.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 13:27:06: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:06: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:08: 4000000 INFO @ Sat, 08 Aug 2020 13:27:14: 1000000 INFO @ Sat, 08 Aug 2020 13:27:17: 5000000 INFO @ Sat, 08 Aug 2020 13:27:21: 2000000 INFO @ Sat, 08 Aug 2020 13:27:25: 6000000 INFO @ Sat, 08 Aug 2020 13:27:29: 3000000 INFO @ Sat, 08 Aug 2020 13:27:33: 7000000 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 13:27:36: 4000000 INFO @ Sat, 08 Aug 2020 13:27:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.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 13:27:36: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:36: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:40: 8000000 INFO @ Sat, 08 Aug 2020 13:27:43: 5000000 INFO @ Sat, 08 Aug 2020 13:27:44: 1000000 INFO @ Sat, 08 Aug 2020 13:27:48: 9000000 INFO @ Sat, 08 Aug 2020 13:27:50: 6000000 INFO @ Sat, 08 Aug 2020 13:27:53: 2000000 INFO @ Sat, 08 Aug 2020 13:27:56: 10000000 INFO @ Sat, 08 Aug 2020 13:27:57: 7000000 INFO @ Sat, 08 Aug 2020 13:28:01: 3000000 INFO @ Sat, 08 Aug 2020 13:28:04: 11000000 INFO @ Sat, 08 Aug 2020 13:28:04: 8000000 INFO @ Sat, 08 Aug 2020 13:28:10: 4000000 INFO @ Sat, 08 Aug 2020 13:28:11: 9000000 INFO @ Sat, 08 Aug 2020 13:28:12: 12000000 INFO @ Sat, 08 Aug 2020 13:28:16: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:16: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:16: #1 total tags in treatment: 5868602 INFO @ Sat, 08 Aug 2020 13:28:16: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:16: #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 13:28:16: #1 tags after filtering in treatment: 5303433 INFO @ Sat, 08 Aug 2020 13:28:16: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:28:16: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:16: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:16: #2 number of paired peaks: 3401 INFO @ Sat, 08 Aug 2020 13:28:16: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:16: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:16: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:16: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:16: #2 predicted fragment length is 239 bps INFO @ Sat, 08 Aug 2020 13:28:16: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 08 Aug 2020 13:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.05_model.r WARNING @ Sat, 08 Aug 2020 13:28:16: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:16: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 08 Aug 2020 13:28:16: #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 13:28:16: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:28:18: 5000000 INFO @ Sat, 08 Aug 2020 13:28:18: 10000000 INFO @ Sat, 08 Aug 2020 13:28:25: 11000000 INFO @ Sat, 08 Aug 2020 13:28:26: 6000000 INFO @ Sat, 08 Aug 2020 13:28:30: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:32: 12000000 INFO @ Sat, 08 Aug 2020 13:28:35: 7000000 INFO @ Sat, 08 Aug 2020 13:28:36: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:36: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:36: #1 total tags in treatment: 5868602 INFO @ Sat, 08 Aug 2020 13:28:36: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:36: #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 13:28:36: #1 tags after filtering in treatment: 5303433 INFO @ Sat, 08 Aug 2020 13:28:36: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:28:36: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:36: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:36: #2 number of paired peaks: 3401 INFO @ Sat, 08 Aug 2020 13:28:36: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:37: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:37: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:37: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:37: #2 predicted fragment length is 239 bps INFO @ Sat, 08 Aug 2020 13:28:37: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 08 Aug 2020 13:28:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.10_model.r WARNING @ Sat, 08 Aug 2020 13:28:37: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:37: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 08 Aug 2020 13:28:37: #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 13:28:37: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:28:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.05_summits.bed INFO @ Sat, 08 Aug 2020 13:28:37: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9882 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:28:43: 8000000 INFO @ Sat, 08 Aug 2020 13:28:50: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:51: 9000000 INFO @ Sat, 08 Aug 2020 13:28:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.10_summits.bed INFO @ Sat, 08 Aug 2020 13:28:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7219 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:28:59: 10000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:29:06: 11000000 INFO @ Sat, 08 Aug 2020 13:29:14: 12000000 INFO @ Sat, 08 Aug 2020 13:29:17: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:29:17: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:29:17: #1 total tags in treatment: 5868602 INFO @ Sat, 08 Aug 2020 13:29:17: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:29:17: #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 13:29:17: #1 tags after filtering in treatment: 5303433 INFO @ Sat, 08 Aug 2020 13:29:17: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:29:17: #1 finished! INFO @ Sat, 08 Aug 2020 13:29:17: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:29:18: #2 number of paired peaks: 3401 INFO @ Sat, 08 Aug 2020 13:29:18: start model_add_line... INFO @ Sat, 08 Aug 2020 13:29:18: start X-correlation... INFO @ Sat, 08 Aug 2020 13:29:18: end of X-cor INFO @ Sat, 08 Aug 2020 13:29:18: #2 finished! INFO @ Sat, 08 Aug 2020 13:29:18: #2 predicted fragment length is 239 bps INFO @ Sat, 08 Aug 2020 13:29:18: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 08 Aug 2020 13:29:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.20_model.r WARNING @ Sat, 08 Aug 2020 13:29:18: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:29:18: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 08 Aug 2020 13:29:18: #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 13:29:18: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:29:32: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392420/SRX8392420.20_summits.bed INFO @ Sat, 08 Aug 2020 13:29:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4253 records, 4 fields): 5 millis CompletedMACS2peakCalling