Job ID = 6367803 SRX = SRX4085371 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:39:29 prefetch.2.10.7: 1) Downloading 'SRR7167400'... 2020-06-15T23:39:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:30 prefetch.2.10.7: 1) 'SRR7167400' was downloaded successfully Read 14631211 spots for SRR7167400/SRR7167400.sra Written 14631211 spots for SRR7167400/SRR7167400.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:03 14631211 reads; of these: 14631211 (100.00%) were paired; of these: 7609572 (52.01%) aligned concordantly 0 times 6227384 (42.56%) aligned concordantly exactly 1 time 794255 (5.43%) aligned concordantly >1 times ---- 7609572 pairs aligned concordantly 0 times; of these: 198195 (2.60%) aligned discordantly 1 time ---- 7411377 pairs aligned 0 times concordantly or discordantly; of these: 14822754 mates make up the pairs; of these: 11486935 (77.50%) aligned 0 times 2963219 (19.99%) aligned exactly 1 time 372600 (2.51%) aligned >1 times 60.75% overall alignment rate Time searching: 00:08:03 Overall time: 00:08:03 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 8 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] 537514 / 7135597 = 0.0753 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 09:00:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.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 09:00:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:59: 1000000 INFO @ Tue, 16 Jun 2020 09:01:04: 2000000 INFO @ Tue, 16 Jun 2020 09:01:09: 3000000 INFO @ Tue, 16 Jun 2020 09:01:14: 4000000 INFO @ Tue, 16 Jun 2020 09:01:19: 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 09:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.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 09:01:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:24: 6000000 INFO @ Tue, 16 Jun 2020 09:01:29: 1000000 INFO @ Tue, 16 Jun 2020 09:01:29: 7000000 INFO @ Tue, 16 Jun 2020 09:01:34: 2000000 INFO @ Tue, 16 Jun 2020 09:01:34: 8000000 INFO @ Tue, 16 Jun 2020 09:01:39: 3000000 INFO @ Tue, 16 Jun 2020 09:01:39: 9000000 INFO @ Tue, 16 Jun 2020 09:01:44: 4000000 INFO @ Tue, 16 Jun 2020 09:01:45: 10000000 INFO @ Tue, 16 Jun 2020 09:01:49: 5000000 INFO @ Tue, 16 Jun 2020 09:01:50: 11000000 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 09:01:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.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 09:01:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:55: 6000000 INFO @ Tue, 16 Jun 2020 09:01:55: 12000000 INFO @ Tue, 16 Jun 2020 09:01:59: 1000000 INFO @ Tue, 16 Jun 2020 09:02:00: 7000000 INFO @ Tue, 16 Jun 2020 09:02:00: 13000000 INFO @ Tue, 16 Jun 2020 09:02:04: 2000000 INFO @ Tue, 16 Jun 2020 09:02:05: 8000000 INFO @ Tue, 16 Jun 2020 09:02:06: 14000000 INFO @ Tue, 16 Jun 2020 09:02:09: 3000000 INFO @ Tue, 16 Jun 2020 09:02:10: 9000000 INFO @ Tue, 16 Jun 2020 09:02:11: 15000000 INFO @ Tue, 16 Jun 2020 09:02:15: 4000000 INFO @ Tue, 16 Jun 2020 09:02:16: 10000000 INFO @ Tue, 16 Jun 2020 09:02:16: 16000000 INFO @ Tue, 16 Jun 2020 09:02:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:20: #1 total tags in treatment: 6490892 INFO @ Tue, 16 Jun 2020 09:02:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:20: #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 09:02:20: #1 tags after filtering in treatment: 5985121 INFO @ Tue, 16 Jun 2020 09:02:20: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:02:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:20: 5000000 INFO @ Tue, 16 Jun 2020 09:02:20: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 09:02:20: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:20: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:02:20: #2 alternative fragment length(s) may be 4,103 bps INFO @ Tue, 16 Jun 2020 09:02:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.05_model.r INFO @ Tue, 16 Jun 2020 09:02:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:21: 11000000 INFO @ Tue, 16 Jun 2020 09:02:25: 6000000 INFO @ Tue, 16 Jun 2020 09:02:26: 12000000 INFO @ Tue, 16 Jun 2020 09:02:31: 7000000 INFO @ Tue, 16 Jun 2020 09:02:31: 13000000 INFO @ Tue, 16 Jun 2020 09:02:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:36: 8000000 INFO @ Tue, 16 Jun 2020 09:02:36: 14000000 INFO @ Tue, 16 Jun 2020 09:02:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.05_summits.bed INFO @ Tue, 16 Jun 2020 09:02:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1357 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:41: 9000000 INFO @ Tue, 16 Jun 2020 09:02:42: 15000000 INFO @ Tue, 16 Jun 2020 09:02:46: 10000000 INFO @ Tue, 16 Jun 2020 09:02:47: 16000000 INFO @ Tue, 16 Jun 2020 09:02:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:50: #1 total tags in treatment: 6490892 INFO @ Tue, 16 Jun 2020 09:02:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:50: #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 09:02:50: #1 tags after filtering in treatment: 5985121 INFO @ Tue, 16 Jun 2020 09:02:50: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:02:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:51: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 09:02:51: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:51: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:02:51: #2 alternative fragment length(s) may be 4,103 bps INFO @ Tue, 16 Jun 2020 09:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.10_model.r INFO @ Tue, 16 Jun 2020 09:02:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:52: 11000000 INFO @ Tue, 16 Jun 2020 09:02:57: 12000000 INFO @ Tue, 16 Jun 2020 09:03:02: 13000000 INFO @ Tue, 16 Jun 2020 09:03:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:07: 14000000 INFO @ Tue, 16 Jun 2020 09:03:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.10_summits.bed INFO @ Tue, 16 Jun 2020 09:03:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (295 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:12: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:03:17: 16000000 INFO @ Tue, 16 Jun 2020 09:03:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:21: #1 total tags in treatment: 6490892 INFO @ Tue, 16 Jun 2020 09:03:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:21: #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 09:03:21: #1 tags after filtering in treatment: 5985121 INFO @ Tue, 16 Jun 2020 09:03:21: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:03:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:21: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 09:03:21: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:21: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:03:21: #2 alternative fragment length(s) may be 4,103 bps INFO @ Tue, 16 Jun 2020 09:03:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.20_model.r INFO @ Tue, 16 Jun 2020 09:03:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085371/SRX4085371.20_summits.bed INFO @ Tue, 16 Jun 2020 09:03:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (70 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。