Job ID = 6497357 SRX = SRX2011725 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:30:49 prefetch.2.10.7: 1) Downloading 'SRR4017967'... 2020-06-25T21:30:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:36:26 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:36:26 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: 00:24:54 14269660 reads; of these: 14269660 (100.00%) were paired; of these: 2011691 (14.10%) aligned concordantly 0 times 10166303 (71.24%) aligned concordantly exactly 1 time 2091666 (14.66%) aligned concordantly >1 times ---- 2011691 pairs aligned concordantly 0 times; of these: 1128378 (56.09%) aligned discordantly 1 time ---- 883313 pairs aligned 0 times concordantly or discordantly; of these: 1766626 mates make up the pairs; of these: 1159548 (65.64%) aligned 0 times 227869 (12.90%) aligned exactly 1 time 379209 (21.47%) aligned >1 times 95.94% overall alignment rate Time searching: 00:24:56 Overall time: 00:24:56 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] 4241020 / 13346658 = 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 07:17:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:17:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:17:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:17:18: 1000000 INFO @ Fri, 26 Jun 2020 07:17:26: 2000000 INFO @ Fri, 26 Jun 2020 07:17:33: 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 @ Fri, 26 Jun 2020 07:17:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:17:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:17:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:17:41: 4000000 INFO @ Fri, 26 Jun 2020 07:17:49: 1000000 INFO @ Fri, 26 Jun 2020 07:17:50: 5000000 INFO @ Fri, 26 Jun 2020 07:17:57: 2000000 INFO @ Fri, 26 Jun 2020 07:17:58: 6000000 INFO @ Fri, 26 Jun 2020 07:18:05: 3000000 INFO @ Fri, 26 Jun 2020 07:18:07: 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 @ Fri, 26 Jun 2020 07:18:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:18:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:18:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:18:14: 4000000 INFO @ Fri, 26 Jun 2020 07:18:15: 8000000 INFO @ Fri, 26 Jun 2020 07:18:18: 1000000 INFO @ Fri, 26 Jun 2020 07:18:22: 5000000 INFO @ Fri, 26 Jun 2020 07:18:24: 9000000 INFO @ Fri, 26 Jun 2020 07:18:25: 2000000 INFO @ Fri, 26 Jun 2020 07:18:31: 6000000 INFO @ Fri, 26 Jun 2020 07:18:33: 10000000 INFO @ Fri, 26 Jun 2020 07:18:33: 3000000 INFO @ Fri, 26 Jun 2020 07:18:39: 7000000 INFO @ Fri, 26 Jun 2020 07:18:40: 4000000 INFO @ Fri, 26 Jun 2020 07:18:41: 11000000 INFO @ Fri, 26 Jun 2020 07:18:48: 5000000 INFO @ Fri, 26 Jun 2020 07:18:48: 8000000 INFO @ Fri, 26 Jun 2020 07:18:49: 12000000 INFO @ Fri, 26 Jun 2020 07:18:56: 6000000 INFO @ Fri, 26 Jun 2020 07:18:57: 9000000 INFO @ Fri, 26 Jun 2020 07:18:58: 13000000 INFO @ Fri, 26 Jun 2020 07:19:03: 7000000 INFO @ Fri, 26 Jun 2020 07:19:05: 10000000 INFO @ Fri, 26 Jun 2020 07:19:06: 14000000 INFO @ Fri, 26 Jun 2020 07:19:11: 8000000 INFO @ Fri, 26 Jun 2020 07:19:14: 11000000 INFO @ Fri, 26 Jun 2020 07:19:15: 15000000 INFO @ Fri, 26 Jun 2020 07:19:18: 9000000 INFO @ Fri, 26 Jun 2020 07:19:22: 12000000 INFO @ Fri, 26 Jun 2020 07:19:24: 16000000 INFO @ Fri, 26 Jun 2020 07:19:26: 10000000 INFO @ Fri, 26 Jun 2020 07:19:30: 13000000 INFO @ Fri, 26 Jun 2020 07:19:32: 17000000 INFO @ Fri, 26 Jun 2020 07:19:33: 11000000 INFO @ Fri, 26 Jun 2020 07:19:39: 14000000 INFO @ Fri, 26 Jun 2020 07:19:40: 18000000 INFO @ Fri, 26 Jun 2020 07:19:40: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:19:47: 15000000 INFO @ Fri, 26 Jun 2020 07:19:48: 13000000 INFO @ Fri, 26 Jun 2020 07:19:48: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 07:19:48: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 07:19:48: #1 total tags in treatment: 8225761 INFO @ Fri, 26 Jun 2020 07:19:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:19:48: #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 07:19:48: #1 tags after filtering in treatment: 7155975 INFO @ Fri, 26 Jun 2020 07:19:48: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 26 Jun 2020 07:19:48: #1 finished! INFO @ Fri, 26 Jun 2020 07:19:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:19:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:19:48: #2 number of paired peaks: 1372 INFO @ Fri, 26 Jun 2020 07:19:48: start model_add_line... INFO @ Fri, 26 Jun 2020 07:19:48: start X-correlation... INFO @ Fri, 26 Jun 2020 07:19:48: end of X-cor INFO @ Fri, 26 Jun 2020 07:19:48: #2 finished! INFO @ Fri, 26 Jun 2020 07:19:48: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 07:19:48: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 07:19:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.05_model.r WARNING @ Fri, 26 Jun 2020 07:19:48: #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 07:19:48: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 26 Jun 2020 07:19:48: #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 07:19:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:19:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:19:55: 14000000 INFO @ Fri, 26 Jun 2020 07:19:56: 16000000 INFO @ Fri, 26 Jun 2020 07:20:02: 15000000 INFO @ Fri, 26 Jun 2020 07:20:04: 17000000 INFO @ Fri, 26 Jun 2020 07:20:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:09: 16000000 INFO @ Fri, 26 Jun 2020 07:20:13: 18000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:20:17: 17000000 INFO @ Fri, 26 Jun 2020 07:20:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.05_summits.bed INFO @ Fri, 26 Jun 2020 07:20:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2637 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:20:20: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 07:20:20: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 07:20:20: #1 total tags in treatment: 8225761 INFO @ Fri, 26 Jun 2020 07:20:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:20: #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 07:20:20: #1 tags after filtering in treatment: 7155975 INFO @ Fri, 26 Jun 2020 07:20:20: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 26 Jun 2020 07:20:20: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:21: #2 number of paired peaks: 1372 INFO @ Fri, 26 Jun 2020 07:20:21: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:21: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:21: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:21: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:21: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 07:20:21: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 07:20:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.10_model.r WARNING @ Fri, 26 Jun 2020 07:20:21: #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 07:20:21: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 26 Jun 2020 07:20:21: #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 07:20:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:20:24: 18000000 INFO @ Fri, 26 Jun 2020 07:20:30: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 07:20:30: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 07:20:30: #1 total tags in treatment: 8225761 INFO @ Fri, 26 Jun 2020 07:20:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:30: #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 07:20:30: #1 tags after filtering in treatment: 7155975 INFO @ Fri, 26 Jun 2020 07:20:30: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 26 Jun 2020 07:20:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:30: #2 number of paired peaks: 1372 INFO @ Fri, 26 Jun 2020 07:20:30: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:30: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:30: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:30: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:30: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 07:20:30: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 07:20:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.20_model.r WARNING @ Fri, 26 Jun 2020 07:20:30: #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 07:20:30: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 26 Jun 2020 07:20:30: #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 07:20:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:20:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.10_summits.bed INFO @ Fri, 26 Jun 2020 07:20:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1274 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:20:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011725/SRX2011725.20_summits.bed INFO @ Fri, 26 Jun 2020 07:20:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (618 records, 4 fields): 2 millis CompletedMACS2peakCalling