Job ID = 6507747 SRX = SRX2011725 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T14:03:42 prefetch.2.10.7: 1) Downloading 'SRR4017967'... 2020-06-26T14:03:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:08:54 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:08:54 prefetch.2.10.7: 1) 'SRR4017967' was downloaded successfully Read 14269660 spots for SRR4017967/SRR4017967.sra Written 14269660 spots for SRR4017967/SRR4017967.sra 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:00 14269660 reads; of these: 14269660 (100.00%) were paired; of these: 2011704 (14.10%) aligned concordantly 0 times 10166249 (71.24%) aligned concordantly exactly 1 time 2091707 (14.66%) aligned concordantly >1 times ---- 2011704 pairs aligned concordantly 0 times; of these: 1128411 (56.09%) aligned discordantly 1 time ---- 883293 pairs aligned 0 times concordantly or discordantly; of these: 1766586 mates make up the pairs; of these: 1159481 (65.63%) aligned 0 times 227864 (12.90%) aligned exactly 1 time 379241 (21.47%) aligned >1 times 95.94% overall alignment rate Time searching: 00:23:01 Overall time: 00:23:01 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] 4240959 / 13346678 = 0.3178 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 @ Fri, 26 Jun 2020 23:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.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 @ Fri, 26 Jun 2020 23:45:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:45:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:45:18: 1000000 INFO @ Fri, 26 Jun 2020 23:45:25: 2000000 INFO @ Fri, 26 Jun 2020 23:45:31: 3000000 INFO @ Fri, 26 Jun 2020 23:45:38: 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 @ Fri, 26 Jun 2020 23:45:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.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 @ Fri, 26 Jun 2020 23:45:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:45:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:45:45: 5000000 INFO @ Fri, 26 Jun 2020 23:45:49: 1000000 INFO @ Fri, 26 Jun 2020 23:45:52: 6000000 INFO @ Fri, 26 Jun 2020 23:45:57: 2000000 INFO @ Fri, 26 Jun 2020 23:46:00: 7000000 INFO @ Fri, 26 Jun 2020 23:46:04: 3000000 INFO @ Fri, 26 Jun 2020 23:46:07: 8000000 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 @ Fri, 26 Jun 2020 23:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.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 @ Fri, 26 Jun 2020 23:46:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:46:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:46:12: 4000000 INFO @ Fri, 26 Jun 2020 23:46:15: 9000000 INFO @ Fri, 26 Jun 2020 23:46:19: 1000000 INFO @ Fri, 26 Jun 2020 23:46:19: 5000000 INFO @ Fri, 26 Jun 2020 23:46:23: 10000000 INFO @ Fri, 26 Jun 2020 23:46:27: 6000000 INFO @ Fri, 26 Jun 2020 23:46:27: 2000000 INFO @ Fri, 26 Jun 2020 23:46:30: 11000000 INFO @ Fri, 26 Jun 2020 23:46:35: 7000000 INFO @ Fri, 26 Jun 2020 23:46:35: 3000000 INFO @ Fri, 26 Jun 2020 23:46:38: 12000000 INFO @ Fri, 26 Jun 2020 23:46:42: 8000000 INFO @ Fri, 26 Jun 2020 23:46:43: 4000000 INFO @ Fri, 26 Jun 2020 23:46:46: 13000000 INFO @ Fri, 26 Jun 2020 23:46:50: 9000000 INFO @ Fri, 26 Jun 2020 23:46:51: 5000000 INFO @ Fri, 26 Jun 2020 23:46:54: 14000000 INFO @ Fri, 26 Jun 2020 23:46:58: 10000000 INFO @ Fri, 26 Jun 2020 23:46:58: 6000000 INFO @ Fri, 26 Jun 2020 23:47:02: 15000000 INFO @ Fri, 26 Jun 2020 23:47:06: 11000000 INFO @ Fri, 26 Jun 2020 23:47:06: 7000000 INFO @ Fri, 26 Jun 2020 23:47:10: 16000000 INFO @ Fri, 26 Jun 2020 23:47:13: 12000000 INFO @ Fri, 26 Jun 2020 23:47:14: 8000000 INFO @ Fri, 26 Jun 2020 23:47:17: 17000000 INFO @ Fri, 26 Jun 2020 23:47:22: 9000000 INFO @ Fri, 26 Jun 2020 23:47:22: 13000000 INFO @ Fri, 26 Jun 2020 23:47:25: 18000000 INFO @ Fri, 26 Jun 2020 23:47:29: 10000000 INFO @ Fri, 26 Jun 2020 23:47:30: 14000000 INFO @ Fri, 26 Jun 2020 23:47:32: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:47:32: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:47:32: #1 total tags in treatment: 8225811 INFO @ Fri, 26 Jun 2020 23:47:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:47:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:47:32: #1 tags after filtering in treatment: 7155966 INFO @ Fri, 26 Jun 2020 23:47:32: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 26 Jun 2020 23:47:32: #1 finished! INFO @ Fri, 26 Jun 2020 23:47:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:47:33: #2 number of paired peaks: 1371 INFO @ Fri, 26 Jun 2020 23:47:33: start model_add_line... INFO @ Fri, 26 Jun 2020 23:47:33: start X-correlation... INFO @ Fri, 26 Jun 2020 23:47:33: end of X-cor INFO @ Fri, 26 Jun 2020 23:47:33: #2 finished! INFO @ Fri, 26 Jun 2020 23:47:33: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 23:47:33: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 23:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.05_model.r WARNING @ Fri, 26 Jun 2020 23:47:33: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:47:33: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 26 Jun 2020 23:47:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:47:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:47:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:47:37: 11000000 INFO @ Fri, 26 Jun 2020 23:47:37: 15000000 INFO @ Fri, 26 Jun 2020 23:47:44: 12000000 INFO @ Fri, 26 Jun 2020 23:47:45: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:47:53: 17000000 INFO @ Fri, 26 Jun 2020 23:47:53: 13000000 INFO @ Fri, 26 Jun 2020 23:47:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:48:00: 18000000 INFO @ Fri, 26 Jun 2020 23:48:01: 14000000 INFO @ Fri, 26 Jun 2020 23:48:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:48:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:48:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.05_summits.bed INFO @ Fri, 26 Jun 2020 23:48:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2638 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:48:07: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:48:07: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:48:07: #1 total tags in treatment: 8225811 INFO @ Fri, 26 Jun 2020 23:48:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:48:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:48:08: #1 tags after filtering in treatment: 7155966 INFO @ Fri, 26 Jun 2020 23:48:08: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 26 Jun 2020 23:48:08: #1 finished! INFO @ Fri, 26 Jun 2020 23:48:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:48:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:48:08: #2 number of paired peaks: 1371 INFO @ Fri, 26 Jun 2020 23:48:08: start model_add_line... INFO @ Fri, 26 Jun 2020 23:48:08: start X-correlation... INFO @ Fri, 26 Jun 2020 23:48:08: end of X-cor INFO @ Fri, 26 Jun 2020 23:48:08: #2 finished! INFO @ Fri, 26 Jun 2020 23:48:08: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 23:48:08: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 23:48:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.10_model.r WARNING @ Fri, 26 Jun 2020 23:48:08: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:48:08: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 26 Jun 2020 23:48:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:48:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:48:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:48:08: 15000000 INFO @ Fri, 26 Jun 2020 23:48:15: 16000000 INFO @ Fri, 26 Jun 2020 23:48:23: 17000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:48:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:48:30: 18000000 INFO @ Fri, 26 Jun 2020 23:48:36: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:48:36: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:48:36: #1 total tags in treatment: 8225811 INFO @ Fri, 26 Jun 2020 23:48:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:48:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:48:36: #1 tags after filtering in treatment: 7155966 INFO @ Fri, 26 Jun 2020 23:48:36: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 26 Jun 2020 23:48:36: #1 finished! INFO @ Fri, 26 Jun 2020 23:48:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:48:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:48:37: #2 number of paired peaks: 1371 INFO @ Fri, 26 Jun 2020 23:48:37: start model_add_line... INFO @ Fri, 26 Jun 2020 23:48:37: start X-correlation... INFO @ Fri, 26 Jun 2020 23:48:37: end of X-cor INFO @ Fri, 26 Jun 2020 23:48:37: #2 finished! INFO @ Fri, 26 Jun 2020 23:48:37: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 23:48:37: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 23:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.20_model.r WARNING @ Fri, 26 Jun 2020 23:48:37: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:48:37: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 26 Jun 2020 23:48:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:48:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.10_summits.bed INFO @ Fri, 26 Jun 2020 23:48:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1275 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:48:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011725/SRX2011725.20_summits.bed INFO @ Fri, 26 Jun 2020 23:49:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 1 millis CompletedMACS2peakCalling