Job ID = 6454841 SRX = SRX2592436 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:35:40 prefetch.2.10.7: 1) Downloading 'SRR5289713'... 2020-06-21T09:35:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:38:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:38:22 prefetch.2.10.7: 'SRR5289713' is valid 2020-06-21T09:38:22 prefetch.2.10.7: 1) 'SRR5289713' was downloaded successfully Read 10054423 spots for SRR5289713/SRR5289713.sra Written 10054423 spots for SRR5289713/SRR5289713.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: 00:02:54 10054423 reads; of these: 10054423 (100.00%) were unpaired; of these: 1009736 (10.04%) aligned 0 times 7870204 (78.28%) aligned exactly 1 time 1174483 (11.68%) aligned >1 times 89.96% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2784821 / 9044687 = 0.3079 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 @ Sun, 21 Jun 2020 18:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:45:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:29: 1000000 INFO @ Sun, 21 Jun 2020 18:45:34: 2000000 INFO @ Sun, 21 Jun 2020 18:45:40: 3000000 INFO @ Sun, 21 Jun 2020 18:45:46: 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 @ Sun, 21 Jun 2020 18:45:52: 5000000 INFO @ Sun, 21 Jun 2020 18:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:45:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:58: 6000000 INFO @ Sun, 21 Jun 2020 18:45:59: 1000000 INFO @ Sun, 21 Jun 2020 18:45:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:59: #1 total tags in treatment: 6259866 INFO @ Sun, 21 Jun 2020 18:45:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:46:00: #1 tags after filtering in treatment: 6259600 INFO @ Sun, 21 Jun 2020 18:46:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:01: #2 number of paired peaks: 470 WARNING @ Sun, 21 Jun 2020 18:46:01: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:01: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 18:46:01: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 18:46:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.05_model.r INFO @ Sun, 21 Jun 2020 18:46:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:04: 2000000 INFO @ Sun, 21 Jun 2020 18:46:09: 3000000 INFO @ Sun, 21 Jun 2020 18:46:15: 4000000 INFO @ Sun, 21 Jun 2020 18:46:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:21: 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 @ Sun, 21 Jun 2020 18:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:46:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:26: 6000000 INFO @ Sun, 21 Jun 2020 18:46:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.05_summits.bed INFO @ Sun, 21 Jun 2020 18:46:28: Done! pass1 - making usageList (249 chroms): 3 millis pass2 - checking and writing primary data (13344 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:46:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:46:28: #1 total tags in treatment: 6259866 INFO @ Sun, 21 Jun 2020 18:46:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:46:29: #1 tags after filtering in treatment: 6259600 INFO @ Sun, 21 Jun 2020 18:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:29: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:29: 1000000 INFO @ Sun, 21 Jun 2020 18:46:30: #2 number of paired peaks: 470 WARNING @ Sun, 21 Jun 2020 18:46:30: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:30: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 18:46:30: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 18:46:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.10_model.r INFO @ Sun, 21 Jun 2020 18:46:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:34: 2000000 INFO @ Sun, 21 Jun 2020 18:46:40: 3000000 INFO @ Sun, 21 Jun 2020 18:46:45: 4000000 INFO @ Sun, 21 Jun 2020 18:46:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:51: 5000000 INFO @ Sun, 21 Jun 2020 18:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.10_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:46:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.10_summits.bed INFO @ Sun, 21 Jun 2020 18:46:56: Done! pass1 - making usageList (193 chroms): 2 millis pass2 - checking and writing primary data (9060 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:57: 6000000 INFO @ Sun, 21 Jun 2020 18:46:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:46:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:46:58: #1 total tags in treatment: 6259866 INFO @ Sun, 21 Jun 2020 18:46:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:46:59: #1 tags after filtering in treatment: 6259600 INFO @ Sun, 21 Jun 2020 18:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:00: #2 number of paired peaks: 470 WARNING @ Sun, 21 Jun 2020 18:47:00: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 21 Jun 2020 18:47:00: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:00: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:00: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:00: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:00: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 18:47:00: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 18:47:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.20_model.r INFO @ Sun, 21 Jun 2020 18:47:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:47:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592436/SRX2592436.20_summits.bed INFO @ Sun, 21 Jun 2020 18:47:25: Done! pass1 - making usageList (127 chroms): 2 millis pass2 - checking and writing primary data (5615 records, 4 fields): 14 millis CompletedMACS2peakCalling