Job ID = 8069382 SRX = SRX7217785 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:31:45 prefetch.2.10.7: 1) Downloading 'SRR10533862'... 2020-08-08T03:31:45 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:33:29 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:33:29 prefetch.2.10.7: 1) 'SRR10533862' was downloaded successfully 2020-08-08T03:33:29 prefetch.2.10.7: 'SRR10533862' has 0 unresolved dependencies Read 7038331 spots for SRR10533862/SRR10533862.sra Written 7038331 spots for SRR10533862/SRR10533862.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070171 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:12 7038331 reads; of these: 7038331 (100.00%) were paired; of these: 991031 (14.08%) aligned concordantly 0 times 5524016 (78.48%) aligned concordantly exactly 1 time 523284 (7.43%) aligned concordantly >1 times ---- 991031 pairs aligned concordantly 0 times; of these: 292487 (29.51%) aligned discordantly 1 time ---- 698544 pairs aligned 0 times concordantly or discordantly; of these: 1397088 mates make up the pairs; of these: 1216500 (87.07%) aligned 0 times 121918 (8.73%) aligned exactly 1 time 58670 (4.20%) aligned >1 times 91.36% overall alignment rate Time searching: 00:11:12 Overall time: 00:11:12 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] 1225390 / 6302802 = 0.1944 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 12:50:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.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 12:50:42: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:50:42: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:50:51: 1000000 INFO @ Sat, 08 Aug 2020 12:51:01: 2000000 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 12:51:10: 3000000 INFO @ Sat, 08 Aug 2020 12:51:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.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 12:51:11: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:51:11: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:51:20: 1000000 INFO @ Sat, 08 Aug 2020 12:51:20: 4000000 INFO @ Sat, 08 Aug 2020 12:51:28: 2000000 INFO @ Sat, 08 Aug 2020 12:51:30: 5000000 INFO @ Sat, 08 Aug 2020 12:51:37: 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 @ Sat, 08 Aug 2020 12:51:41: 6000000 INFO @ Sat, 08 Aug 2020 12:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.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 12:51:41: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:51:41: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:51:46: 4000000 INFO @ Sat, 08 Aug 2020 12:51:51: 7000000 INFO @ Sat, 08 Aug 2020 12:51:51: 1000000 INFO @ Sat, 08 Aug 2020 12:51:55: 5000000 INFO @ Sat, 08 Aug 2020 12:52:01: 8000000 INFO @ Sat, 08 Aug 2020 12:52:02: 2000000 INFO @ Sat, 08 Aug 2020 12:52:03: 6000000 INFO @ Sat, 08 Aug 2020 12:52:12: 9000000 INFO @ Sat, 08 Aug 2020 12:52:12: 7000000 INFO @ Sat, 08 Aug 2020 12:52:13: 3000000 INFO @ Sat, 08 Aug 2020 12:52:21: 8000000 INFO @ Sat, 08 Aug 2020 12:52:22: 10000000 INFO @ Sat, 08 Aug 2020 12:52:23: 4000000 INFO @ Sat, 08 Aug 2020 12:52:26: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:52:26: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:52:26: #1 total tags in treatment: 4855287 INFO @ Sat, 08 Aug 2020 12:52:26: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:52:26: #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 12:52:26: #1 tags after filtering in treatment: 4309762 INFO @ Sat, 08 Aug 2020 12:52:26: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:52:26: #1 finished! INFO @ Sat, 08 Aug 2020 12:52:26: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:52:27: #2 number of paired peaks: 3152 INFO @ Sat, 08 Aug 2020 12:52:27: start model_add_line... INFO @ Sat, 08 Aug 2020 12:52:27: start X-correlation... INFO @ Sat, 08 Aug 2020 12:52:27: end of X-cor INFO @ Sat, 08 Aug 2020 12:52:27: #2 finished! INFO @ Sat, 08 Aug 2020 12:52:27: #2 predicted fragment length is 239 bps INFO @ Sat, 08 Aug 2020 12:52:27: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 08 Aug 2020 12:52:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.05_model.r WARNING @ Sat, 08 Aug 2020 12:52:27: #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 12:52:27: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 08 Aug 2020 12:52:27: #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 12:52:27: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:52:30: 9000000 INFO @ Sat, 08 Aug 2020 12:52:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:52:38: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:52:38: 10000000 INFO @ Sat, 08 Aug 2020 12:52:42: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:52:42: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:52:42: #1 total tags in treatment: 4855287 INFO @ Sat, 08 Aug 2020 12:52:42: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:52:42: #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 12:52:42: #1 tags after filtering in treatment: 4309762 INFO @ Sat, 08 Aug 2020 12:52:42: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:52:42: #1 finished! INFO @ Sat, 08 Aug 2020 12:52:42: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:52:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:52:42: #2 number of paired peaks: 3152 INFO @ Sat, 08 Aug 2020 12:52:42: start model_add_line... INFO @ Sat, 08 Aug 2020 12:52:43: start X-correlation... INFO @ Sat, 08 Aug 2020 12:52:43: end of X-cor INFO @ Sat, 08 Aug 2020 12:52:43: #2 finished! INFO @ Sat, 08 Aug 2020 12:52:43: #2 predicted fragment length is 239 bps INFO @ Sat, 08 Aug 2020 12:52:43: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 08 Aug 2020 12:52:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.10_model.r WARNING @ Sat, 08 Aug 2020 12:52:43: #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 12:52:43: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 08 Aug 2020 12:52:43: #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 12:52:43: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:52:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:52:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:52:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:52:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.05_summits.bed INFO @ Sat, 08 Aug 2020 12:52:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7491 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:52:44: 6000000 INFO @ Sat, 08 Aug 2020 12:52:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:52:54: 7000000 INFO @ Sat, 08 Aug 2020 12:52:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:52:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:52:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.10_summits.bed INFO @ Sat, 08 Aug 2020 12:52:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5181 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:53:03: 8000000 INFO @ Sat, 08 Aug 2020 12:53:12: 9000000 INFO @ Sat, 08 Aug 2020 12:53:22: 10000000 INFO @ Sat, 08 Aug 2020 12:53:26: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:53:26: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:53:26: #1 total tags in treatment: 4855287 INFO @ Sat, 08 Aug 2020 12:53:26: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:53:26: #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 12:53:26: #1 tags after filtering in treatment: 4309762 INFO @ Sat, 08 Aug 2020 12:53:26: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:53:26: #1 finished! INFO @ Sat, 08 Aug 2020 12:53:26: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:53:26: #2 number of paired peaks: 3152 INFO @ Sat, 08 Aug 2020 12:53:26: start model_add_line... INFO @ Sat, 08 Aug 2020 12:53:26: start X-correlation... INFO @ Sat, 08 Aug 2020 12:53:26: end of X-cor INFO @ Sat, 08 Aug 2020 12:53:26: #2 finished! INFO @ Sat, 08 Aug 2020 12:53:26: #2 predicted fragment length is 239 bps INFO @ Sat, 08 Aug 2020 12:53:26: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 08 Aug 2020 12:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.20_model.r WARNING @ Sat, 08 Aug 2020 12:53:26: #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 12:53:26: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 08 Aug 2020 12:53:26: #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 12:53:26: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:53:37: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:53:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:53:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:53:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217785/SRX7217785.20_summits.bed INFO @ Sat, 08 Aug 2020 12:53:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2745 records, 4 fields): 4 millis CompletedMACS2peakCalling