Job ID = 6367825 SRX = SRX4085393 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:40:14 prefetch.2.10.7: 1) Downloading 'SRR7167422'... 2020-06-15T23:40:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:27 prefetch.2.10.7: 1) 'SRR7167422' was downloaded successfully Read 29930971 spots for SRR7167422/SRR7167422.sra Written 29930971 spots for SRR7167422/SRR7167422.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: 00:21:41 29930971 reads; of these: 29930971 (100.00%) were paired; of these: 2546145 (8.51%) aligned concordantly 0 times 25262483 (84.40%) aligned concordantly exactly 1 time 2122343 (7.09%) aligned concordantly >1 times ---- 2546145 pairs aligned concordantly 0 times; of these: 169115 (6.64%) aligned discordantly 1 time ---- 2377030 pairs aligned 0 times concordantly or discordantly; of these: 4754060 mates make up the pairs; of these: 3808816 (80.12%) aligned 0 times 752441 (15.83%) aligned exactly 1 time 192803 (4.06%) aligned >1 times 93.64% overall alignment rate Time searching: 00:21:42 Overall time: 00:21:42 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 24 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] 22232673 / 27480839 = 0.8090 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 09:27:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.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 09:27:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:34: 1000000 INFO @ Tue, 16 Jun 2020 09:27:41: 2000000 INFO @ Tue, 16 Jun 2020 09:27:48: 3000000 INFO @ Tue, 16 Jun 2020 09:27:54: 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 @ Tue, 16 Jun 2020 09:27:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.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 09:27:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:02: 5000000 INFO @ Tue, 16 Jun 2020 09:28:05: 1000000 INFO @ Tue, 16 Jun 2020 09:28:09: 6000000 INFO @ Tue, 16 Jun 2020 09:28:13: 2000000 INFO @ Tue, 16 Jun 2020 09:28:17: 7000000 INFO @ Tue, 16 Jun 2020 09:28:20: 3000000 INFO @ Tue, 16 Jun 2020 09:28:24: 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 @ Tue, 16 Jun 2020 09:28:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.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 09:28:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:27: 4000000 INFO @ Tue, 16 Jun 2020 09:28:31: 9000000 INFO @ Tue, 16 Jun 2020 09:28:34: 1000000 INFO @ Tue, 16 Jun 2020 09:28:35: 5000000 INFO @ Tue, 16 Jun 2020 09:28:39: 10000000 INFO @ Tue, 16 Jun 2020 09:28:41: 2000000 INFO @ Tue, 16 Jun 2020 09:28:42: 6000000 INFO @ Tue, 16 Jun 2020 09:28:46: 11000000 INFO @ Tue, 16 Jun 2020 09:28:48: 3000000 INFO @ Tue, 16 Jun 2020 09:28:49: 7000000 INFO @ Tue, 16 Jun 2020 09:28:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:28:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:28:50: #1 total tags in treatment: 5223372 INFO @ Tue, 16 Jun 2020 09:28:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:50: #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 09:28:50: #1 tags after filtering in treatment: 4147095 INFO @ Tue, 16 Jun 2020 09:28:50: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 16 Jun 2020 09:28:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:51: #2 number of paired peaks: 601 WARNING @ Tue, 16 Jun 2020 09:28:51: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:51: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 09:28:51: #2 alternative fragment length(s) may be 4,156,159 bps INFO @ Tue, 16 Jun 2020 09:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.05_model.r INFO @ Tue, 16 Jun 2020 09:28:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:55: 4000000 INFO @ Tue, 16 Jun 2020 09:28:57: 8000000 INFO @ Tue, 16 Jun 2020 09:29:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:02: 5000000 INFO @ Tue, 16 Jun 2020 09:29:04: 9000000 INFO @ Tue, 16 Jun 2020 09:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (515 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:09: 6000000 INFO @ Tue, 16 Jun 2020 09:29:11: 10000000 INFO @ Tue, 16 Jun 2020 09:29:16: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:18: 11000000 INFO @ Tue, 16 Jun 2020 09:29:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:22: #1 total tags in treatment: 5223372 INFO @ Tue, 16 Jun 2020 09:29:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:22: #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 09:29:22: #1 tags after filtering in treatment: 4147095 INFO @ Tue, 16 Jun 2020 09:29:22: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 16 Jun 2020 09:29:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:23: 8000000 INFO @ Tue, 16 Jun 2020 09:29:23: #2 number of paired peaks: 601 WARNING @ Tue, 16 Jun 2020 09:29:23: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:23: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 09:29:23: #2 alternative fragment length(s) may be 4,156,159 bps INFO @ Tue, 16 Jun 2020 09:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.10_model.r INFO @ Tue, 16 Jun 2020 09:29:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:28: 9000000 INFO @ Tue, 16 Jun 2020 09:29:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:34: 10000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.10_summits.bed INFO @ Tue, 16 Jun 2020 09:29:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:40: 11000000 INFO @ Tue, 16 Jun 2020 09:29:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:43: #1 total tags in treatment: 5223372 INFO @ Tue, 16 Jun 2020 09:29:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:43: #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 09:29:43: #1 tags after filtering in treatment: 4147095 INFO @ Tue, 16 Jun 2020 09:29:43: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 16 Jun 2020 09:29:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:44: #2 number of paired peaks: 601 WARNING @ Tue, 16 Jun 2020 09:29:44: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:44: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 09:29:44: #2 alternative fragment length(s) may be 4,156,159 bps INFO @ Tue, 16 Jun 2020 09:29:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.20_model.r INFO @ Tue, 16 Jun 2020 09:29:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085393/SRX4085393.20_summits.bed INFO @ Tue, 16 Jun 2020 09:29:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 1 millis CompletedMACS2peakCalling