Job ID = 8069398 SRX = SRX7217790 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:31:59 prefetch.2.10.7: 1) Downloading 'SRR10533867'... 2020-08-08T03:31:59 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:53 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:53 prefetch.2.10.7: 1) 'SRR10533867' was downloaded successfully 2020-08-08T03:34:53 prefetch.2.10.7: 'SRR10533867' has 0 unresolved dependencies Read 8389572 spots for SRR10533867/SRR10533867.sra Written 8389572 spots for SRR10533867/SRR10533867.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070444 ("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: 00:15:15 8389572 reads; of these: 8389572 (100.00%) were paired; of these: 1326134 (15.81%) aligned concordantly 0 times 6023786 (71.80%) aligned concordantly exactly 1 time 1039652 (12.39%) aligned concordantly >1 times ---- 1326134 pairs aligned concordantly 0 times; of these: 472557 (35.63%) aligned discordantly 1 time ---- 853577 pairs aligned 0 times concordantly or discordantly; of these: 1707154 mates make up the pairs; of these: 1466905 (85.93%) aligned 0 times 102539 (6.01%) aligned exactly 1 time 137710 (8.07%) aligned >1 times 91.26% overall alignment rate Time searching: 00:15:15 Overall time: 00:15:15 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] 2129978 / 7500680 = 0.2840 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 12:56:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.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 12:56:49: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:49: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:56: 1000000 INFO @ Sat, 08 Aug 2020 12:57:02: 2000000 INFO @ Sat, 08 Aug 2020 12:57:09: 3000000 INFO @ Sat, 08 Aug 2020 12:57:15: 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 @ Sat, 08 Aug 2020 12:57:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.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 12:57:19: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:19: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:22: 5000000 INFO @ Sat, 08 Aug 2020 12:57:26: 1000000 INFO @ Sat, 08 Aug 2020 12:57:28: 6000000 INFO @ Sat, 08 Aug 2020 12:57:33: 2000000 INFO @ Sat, 08 Aug 2020 12:57:35: 7000000 INFO @ Sat, 08 Aug 2020 12:57:39: 3000000 INFO @ Sat, 08 Aug 2020 12:57:41: 8000000 INFO @ Sat, 08 Aug 2020 12:57:46: 4000000 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 12:57:48: 9000000 INFO @ Sat, 08 Aug 2020 12:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.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 12:57:49: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:49: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:53: 5000000 INFO @ Sat, 08 Aug 2020 12:57:55: 10000000 INFO @ Sat, 08 Aug 2020 12:57:56: 1000000 INFO @ Sat, 08 Aug 2020 12:58:00: 6000000 INFO @ Sat, 08 Aug 2020 12:58:01: 11000000 INFO @ Sat, 08 Aug 2020 12:58:02: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:02: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:02: #1 total tags in treatment: 4997944 INFO @ Sat, 08 Aug 2020 12:58:02: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:02: #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 12:58:02: #1 tags after filtering in treatment: 4496689 INFO @ Sat, 08 Aug 2020 12:58:02: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:58:02: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:02: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:02: #2 number of paired peaks: 764 WARNING @ Sat, 08 Aug 2020 12:58:02: Fewer paired peaks (764) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 764 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:02: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:02: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:02: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:02: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:02: #2 predicted fragment length is 212 bps INFO @ Sat, 08 Aug 2020 12:58:02: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 08 Aug 2020 12:58:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.05_model.r WARNING @ Sat, 08 Aug 2020 12:58:02: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:02: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 08 Aug 2020 12:58:02: #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 12:58:02: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:02: 2000000 INFO @ Sat, 08 Aug 2020 12:58:07: 7000000 INFO @ Sat, 08 Aug 2020 12:58:09: 3000000 INFO @ Sat, 08 Aug 2020 12:58:12: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:14: 8000000 INFO @ Sat, 08 Aug 2020 12:58:16: 4000000 INFO @ Sat, 08 Aug 2020 12:58:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.05_summits.bed INFO @ Sat, 08 Aug 2020 12:58:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2366 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:21: 9000000 INFO @ Sat, 08 Aug 2020 12:58:23: 5000000 INFO @ Sat, 08 Aug 2020 12:58:28: 10000000 INFO @ Sat, 08 Aug 2020 12:58:29: 6000000 INFO @ Sat, 08 Aug 2020 12:58:34: 11000000 INFO @ Sat, 08 Aug 2020 12:58:35: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:35: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:35: #1 total tags in treatment: 4997944 INFO @ Sat, 08 Aug 2020 12:58:35: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:35: #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 12:58:35: #1 tags after filtering in treatment: 4496689 INFO @ Sat, 08 Aug 2020 12:58:35: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:58:35: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:35: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:35: #2 number of paired peaks: 764 WARNING @ Sat, 08 Aug 2020 12:58:35: Fewer paired peaks (764) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 764 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:35: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:35: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:35: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:35: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:35: #2 predicted fragment length is 212 bps INFO @ Sat, 08 Aug 2020 12:58:35: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 08 Aug 2020 12:58:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.10_model.r WARNING @ Sat, 08 Aug 2020 12:58:35: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:35: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 08 Aug 2020 12:58:35: #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 12:58:35: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:36: 7000000 INFO @ Sat, 08 Aug 2020 12:58:42: 8000000 INFO @ Sat, 08 Aug 2020 12:58:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:58:49: 9000000 INFO @ Sat, 08 Aug 2020 12:58:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.10_summits.bed INFO @ Sat, 08 Aug 2020 12:58:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1128 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:55: 10000000 INFO @ Sat, 08 Aug 2020 12:59:02: 11000000 INFO @ Sat, 08 Aug 2020 12:59:02: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:02: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:02: #1 total tags in treatment: 4997944 INFO @ Sat, 08 Aug 2020 12:59:02: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:02: #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 12:59:02: #1 tags after filtering in treatment: 4496689 INFO @ Sat, 08 Aug 2020 12:59:02: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:59:02: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:02: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:03: #2 number of paired peaks: 764 WARNING @ Sat, 08 Aug 2020 12:59:03: Fewer paired peaks (764) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 764 pairs to build model! INFO @ Sat, 08 Aug 2020 12:59:03: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:03: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:03: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:03: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:03: #2 predicted fragment length is 212 bps INFO @ Sat, 08 Aug 2020 12:59:03: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 08 Aug 2020 12:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.20_model.r WARNING @ Sat, 08 Aug 2020 12:59:03: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:03: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 08 Aug 2020 12:59:03: #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 12:59:03: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:59:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217790/SRX7217790.20_summits.bed INFO @ Sat, 08 Aug 2020 12:59:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (472 records, 4 fields): 3 millis CompletedMACS2peakCalling