Job ID = 6365823 SRX = ERX1485064 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T21:59:28 prefetch.2.10.7: 1) Downloading 'ERR1414281'... 2020-06-15T21:59:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:04:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:04:41 prefetch.2.10.7: 1) 'ERR1414281' was downloaded successfully Read 13688347 spots for ERR1414281/ERR1414281.sra Written 13688347 spots for ERR1414281/ERR1414281.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:28:00 13688347 reads; of these: 13688347 (100.00%) were paired; of these: 471734 (3.45%) aligned concordantly 0 times 9923392 (72.50%) aligned concordantly exactly 1 time 3293221 (24.06%) aligned concordantly >1 times ---- 471734 pairs aligned concordantly 0 times; of these: 67739 (14.36%) aligned discordantly 1 time ---- 403995 pairs aligned 0 times concordantly or discordantly; of these: 807990 mates make up the pairs; of these: 412879 (51.10%) aligned 0 times 211091 (26.13%) aligned exactly 1 time 184020 (22.78%) aligned >1 times 98.49% overall alignment rate Time searching: 00:28:02 Overall time: 00:28:02 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] 4248320 / 13240590 = 0.3209 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 @ Tue, 16 Jun 2020 07:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.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 @ Tue, 16 Jun 2020 07:44:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:04: 1000000 INFO @ Tue, 16 Jun 2020 07:45:11: 2000000 INFO @ Tue, 16 Jun 2020 07:45:18: 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 @ Tue, 16 Jun 2020 07:45:25: 4000000 INFO @ Tue, 16 Jun 2020 07:45:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.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 @ Tue, 16 Jun 2020 07:45:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:32: 5000000 INFO @ Tue, 16 Jun 2020 07:45:35: 1000000 INFO @ Tue, 16 Jun 2020 07:45:40: 6000000 INFO @ Tue, 16 Jun 2020 07:45:42: 2000000 INFO @ Tue, 16 Jun 2020 07:45:48: 7000000 INFO @ Tue, 16 Jun 2020 07:45:50: 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 @ Tue, 16 Jun 2020 07:45:56: 8000000 INFO @ Tue, 16 Jun 2020 07:45:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.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 @ Tue, 16 Jun 2020 07:45:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:58: 4000000 INFO @ Tue, 16 Jun 2020 07:46:03: 9000000 INFO @ Tue, 16 Jun 2020 07:46:05: 1000000 INFO @ Tue, 16 Jun 2020 07:46:06: 5000000 INFO @ Tue, 16 Jun 2020 07:46:11: 10000000 INFO @ Tue, 16 Jun 2020 07:46:13: 2000000 INFO @ Tue, 16 Jun 2020 07:46:14: 6000000 INFO @ Tue, 16 Jun 2020 07:46:19: 11000000 INFO @ Tue, 16 Jun 2020 07:46:21: 3000000 INFO @ Tue, 16 Jun 2020 07:46:21: 7000000 INFO @ Tue, 16 Jun 2020 07:46:27: 12000000 INFO @ Tue, 16 Jun 2020 07:46:29: 4000000 INFO @ Tue, 16 Jun 2020 07:46:29: 8000000 INFO @ Tue, 16 Jun 2020 07:46:35: 13000000 INFO @ Tue, 16 Jun 2020 07:46:37: 5000000 INFO @ Tue, 16 Jun 2020 07:46:37: 9000000 INFO @ Tue, 16 Jun 2020 07:46:43: 14000000 INFO @ Tue, 16 Jun 2020 07:46:45: 10000000 INFO @ Tue, 16 Jun 2020 07:46:46: 6000000 INFO @ Tue, 16 Jun 2020 07:46:51: 15000000 INFO @ Tue, 16 Jun 2020 07:46:53: 11000000 INFO @ Tue, 16 Jun 2020 07:46:54: 7000000 INFO @ Tue, 16 Jun 2020 07:46:59: 16000000 INFO @ Tue, 16 Jun 2020 07:47:01: 12000000 INFO @ Tue, 16 Jun 2020 07:47:02: 8000000 INFO @ Tue, 16 Jun 2020 07:47:07: 17000000 INFO @ Tue, 16 Jun 2020 07:47:09: 13000000 INFO @ Tue, 16 Jun 2020 07:47:10: 9000000 INFO @ Tue, 16 Jun 2020 07:47:15: 18000000 INFO @ Tue, 16 Jun 2020 07:47:17: 14000000 INFO @ Tue, 16 Jun 2020 07:47:19: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 07:47:19: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 07:47:19: #1 total tags in treatment: 8979403 INFO @ Tue, 16 Jun 2020 07:47:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:47:19: #1 tags after filtering in treatment: 7194304 INFO @ Tue, 16 Jun 2020 07:47:19: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 07:47:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:19: 10000000 INFO @ Tue, 16 Jun 2020 07:47:19: #2 number of paired peaks: 1402 INFO @ Tue, 16 Jun 2020 07:47:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:19: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 07:47:19: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 07:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.05_model.r WARNING @ Tue, 16 Jun 2020 07:47:19: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:47:19: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Tue, 16 Jun 2020 07:47:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:47:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:25: 15000000 INFO @ Tue, 16 Jun 2020 07:47:27: 11000000 INFO @ Tue, 16 Jun 2020 07:47:33: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:47:36: 12000000 INFO @ Tue, 16 Jun 2020 07:47:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:42: 17000000 INFO @ Tue, 16 Jun 2020 07:47:44: 13000000 INFO @ Tue, 16 Jun 2020 07:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:50: 18000000 INFO @ Tue, 16 Jun 2020 07:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.05_summits.bed INFO @ Tue, 16 Jun 2020 07:47:50: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (24320 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:47:52: 14000000 INFO @ Tue, 16 Jun 2020 07:47:53: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 07:47:53: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 07:47:53: #1 total tags in treatment: 8979403 INFO @ Tue, 16 Jun 2020 07:47:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:47:53: #1 tags after filtering in treatment: 7194304 INFO @ Tue, 16 Jun 2020 07:47:53: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 07:47:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:54: #2 number of paired peaks: 1402 INFO @ Tue, 16 Jun 2020 07:47:54: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:54: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:54: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:54: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:54: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 07:47:54: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 07:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.10_model.r WARNING @ Tue, 16 Jun 2020 07:47:54: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:47:54: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Tue, 16 Jun 2020 07:47:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:47:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:59: 15000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:48:06: 16000000 INFO @ Tue, 16 Jun 2020 07:48:13: 17000000 INFO @ Tue, 16 Jun 2020 07:48:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:20: 18000000 INFO @ Tue, 16 Jun 2020 07:48:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:23: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 07:48:23: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 07:48:23: #1 total tags in treatment: 8979403 INFO @ Tue, 16 Jun 2020 07:48:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:48:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.10_summits.bed INFO @ Tue, 16 Jun 2020 07:48:23: Done! INFO @ Tue, 16 Jun 2020 07:48:23: #1 tags after filtering in treatment: 7194304 INFO @ Tue, 16 Jun 2020 07:48:23: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 07:48:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:23: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (15181 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:48:24: #2 number of paired peaks: 1402 INFO @ Tue, 16 Jun 2020 07:48:24: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:24: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:24: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:24: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:24: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 07:48:24: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 07:48:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.20_model.r WARNING @ Tue, 16 Jun 2020 07:48:24: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:48:24: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Tue, 16 Jun 2020 07:48:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:48:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:48:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1485064/ERX1485064.20_summits.bed INFO @ Tue, 16 Jun 2020 07:48:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4663 records, 4 fields): 5 millis CompletedMACS2peakCalling