Job ID = 6367813 SRX = SRX4085381 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:41:44 prefetch.2.10.7: 1) Downloading 'SRR7167410'... 2020-06-15T23:41:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:40 prefetch.2.10.7: 1) 'SRR7167410' was downloaded successfully Read 12127763 spots for SRR7167410/SRR7167410.sra Written 12127763 spots for SRR7167410/SRR7167410.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: 00:05:25 12127763 reads; of these: 12127763 (100.00%) were paired; of these: 10401429 (85.77%) aligned concordantly 0 times 1503240 (12.40%) aligned concordantly exactly 1 time 223094 (1.84%) aligned concordantly >1 times ---- 10401429 pairs aligned concordantly 0 times; of these: 260930 (2.51%) aligned discordantly 1 time ---- 10140499 pairs aligned 0 times concordantly or discordantly; of these: 20280998 mates make up the pairs; of these: 14591510 (71.95%) aligned 0 times 5018352 (24.74%) aligned exactly 1 time 671136 (3.31%) aligned >1 times 39.84% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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_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] 112452 / 1824639 = 0.0616 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 08:57:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.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 08:57:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:27: 1000000 INFO @ Tue, 16 Jun 2020 08:57:32: 2000000 INFO @ Tue, 16 Jun 2020 08:57:37: 3000000 INFO @ Tue, 16 Jun 2020 08:57:42: 4000000 INFO @ Tue, 16 Jun 2020 08:57:48: 5000000 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 08:57:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.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 08:57:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:53: 6000000 INFO @ Tue, 16 Jun 2020 08:57:57: 1000000 INFO @ Tue, 16 Jun 2020 08:57:58: 7000000 INFO @ Tue, 16 Jun 2020 08:58:03: 2000000 INFO @ Tue, 16 Jun 2020 08:58:04: 8000000 INFO @ Tue, 16 Jun 2020 08:58:08: 3000000 INFO @ Tue, 16 Jun 2020 08:58:10: 9000000 INFO @ Tue, 16 Jun 2020 08:58:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:58:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:58:12: #1 total tags in treatment: 1617500 INFO @ Tue, 16 Jun 2020 08:58:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:12: #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 08:58:12: #1 tags after filtering in treatment: 1570272 INFO @ Tue, 16 Jun 2020 08:58:12: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 16 Jun 2020 08:58:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:12: #2 number of paired peaks: 290 WARNING @ Tue, 16 Jun 2020 08:58:12: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:12: #2 predicted fragment length is 171 bps INFO @ Tue, 16 Jun 2020 08:58:12: #2 alternative fragment length(s) may be 100,171,227,256 bps INFO @ Tue, 16 Jun 2020 08:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.05_model.r INFO @ Tue, 16 Jun 2020 08:58:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:14: 4000000 INFO @ Tue, 16 Jun 2020 08:58:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.05_summits.bed INFO @ Tue, 16 Jun 2020 08:58:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (175 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:19: 5000000 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 08:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.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 08:58:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:24: 6000000 INFO @ Tue, 16 Jun 2020 08:58:28: 1000000 INFO @ Tue, 16 Jun 2020 08:58:30: 7000000 INFO @ Tue, 16 Jun 2020 08:58:33: 2000000 INFO @ Tue, 16 Jun 2020 08:58:35: 8000000 INFO @ Tue, 16 Jun 2020 08:58:39: 3000000 INFO @ Tue, 16 Jun 2020 08:58:41: 9000000 INFO @ Tue, 16 Jun 2020 08:58:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:58:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:58:43: #1 total tags in treatment: 1617500 INFO @ Tue, 16 Jun 2020 08:58:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:43: #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 08:58:43: #1 tags after filtering in treatment: 1570272 INFO @ Tue, 16 Jun 2020 08:58:43: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 16 Jun 2020 08:58:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:43: #2 number of paired peaks: 290 WARNING @ Tue, 16 Jun 2020 08:58:43: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:43: #2 predicted fragment length is 171 bps INFO @ Tue, 16 Jun 2020 08:58:43: #2 alternative fragment length(s) may be 100,171,227,256 bps INFO @ Tue, 16 Jun 2020 08:58:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.10_model.r INFO @ Tue, 16 Jun 2020 08:58:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:44: 4000000 INFO @ Tue, 16 Jun 2020 08:58:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (94 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:49: 5000000 INFO @ Tue, 16 Jun 2020 08:58:54: 6000000 INFO @ Tue, 16 Jun 2020 08:58:59: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:59:04: 8000000 INFO @ Tue, 16 Jun 2020 08:59:09: 9000000 INFO @ Tue, 16 Jun 2020 08:59:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:59:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:59:11: #1 total tags in treatment: 1617500 INFO @ Tue, 16 Jun 2020 08:59:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:11: #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 08:59:11: #1 tags after filtering in treatment: 1570272 INFO @ Tue, 16 Jun 2020 08:59:11: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 16 Jun 2020 08:59:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:11: #2 number of paired peaks: 290 WARNING @ Tue, 16 Jun 2020 08:59:11: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 16 Jun 2020 08:59:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:11: #2 predicted fragment length is 171 bps INFO @ Tue, 16 Jun 2020 08:59:11: #2 alternative fragment length(s) may be 100,171,227,256 bps INFO @ Tue, 16 Jun 2020 08:59:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.20_model.r INFO @ Tue, 16 Jun 2020 08:59:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085381/SRX4085381.20_summits.bed INFO @ Tue, 16 Jun 2020 08:59:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。