Job ID = 6454995 SRX = SRX2618531 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:38:40 prefetch.2.10.7: 1) Downloading 'SRR5319085'... 2020-06-21T09:38:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:40:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:40:28 prefetch.2.10.7: 'SRR5319085' is valid 2020-06-21T09:40:28 prefetch.2.10.7: 1) 'SRR5319085' was downloaded successfully 2020-06-21T09:40:28 prefetch.2.10.7: 'SRR5319085' has 0 unresolved dependencies Read 14834287 spots for SRR5319085/SRR5319085.sra Written 14834287 spots for SRR5319085/SRR5319085.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: 00:03:56 14834287 reads; of these: 14834287 (100.00%) were unpaired; of these: 866204 (5.84%) aligned 0 times 10596009 (71.43%) aligned exactly 1 time 3372074 (22.73%) aligned >1 times 94.16% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1773308 / 13968083 = 0.1270 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 18:48:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.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 18:48:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:59: 1000000 INFO @ Sun, 21 Jun 2020 18:49:04: 2000000 INFO @ Sun, 21 Jun 2020 18:49:09: 3000000 INFO @ Sun, 21 Jun 2020 18:49:14: 4000000 INFO @ Sun, 21 Jun 2020 18:49:19: 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 @ Sun, 21 Jun 2020 18:49:24: 6000000 INFO @ Sun, 21 Jun 2020 18:49:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.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 18:49:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:29: 7000000 INFO @ Sun, 21 Jun 2020 18:49:29: 1000000 INFO @ Sun, 21 Jun 2020 18:49:35: 8000000 INFO @ Sun, 21 Jun 2020 18:49:35: 2000000 INFO @ Sun, 21 Jun 2020 18:49:40: 9000000 INFO @ Sun, 21 Jun 2020 18:49:40: 3000000 INFO @ Sun, 21 Jun 2020 18:49:45: 4000000 INFO @ Sun, 21 Jun 2020 18:49:45: 10000000 INFO @ Sun, 21 Jun 2020 18:49:51: 5000000 INFO @ Sun, 21 Jun 2020 18:49:51: 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 @ Sun, 21 Jun 2020 18:49:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.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 18:49:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:56: 6000000 INFO @ Sun, 21 Jun 2020 18:49:56: 12000000 INFO @ Sun, 21 Jun 2020 18:49:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:49:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:49:57: #1 total tags in treatment: 12194775 INFO @ Sun, 21 Jun 2020 18:49:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:57: #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 18:49:58: #1 tags after filtering in treatment: 12194775 INFO @ Sun, 21 Jun 2020 18:49:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:59: #2 number of paired peaks: 831 WARNING @ Sun, 21 Jun 2020 18:49:59: Fewer paired peaks (831) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 831 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:59: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 18:49:59: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 18:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.05_model.r INFO @ Sun, 21 Jun 2020 18:49:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:00: 1000000 INFO @ Sun, 21 Jun 2020 18:50:01: 7000000 INFO @ Sun, 21 Jun 2020 18:50:05: 2000000 INFO @ Sun, 21 Jun 2020 18:50:07: 8000000 INFO @ Sun, 21 Jun 2020 18:50:11: 3000000 INFO @ Sun, 21 Jun 2020 18:50:12: 9000000 INFO @ Sun, 21 Jun 2020 18:50:16: 4000000 INFO @ Sun, 21 Jun 2020 18:50:18: 10000000 INFO @ Sun, 21 Jun 2020 18:50:21: 5000000 INFO @ Sun, 21 Jun 2020 18:50:23: 11000000 INFO @ Sun, 21 Jun 2020 18:50:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:26: 6000000 INFO @ Sun, 21 Jun 2020 18:50:29: 12000000 INFO @ Sun, 21 Jun 2020 18:50:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:50:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:50:30: #1 total tags in treatment: 12194775 INFO @ Sun, 21 Jun 2020 18:50:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:30: #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 18:50:30: #1 tags after filtering in treatment: 12194775 INFO @ Sun, 21 Jun 2020 18:50:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:31: #2 number of paired peaks: 831 WARNING @ Sun, 21 Jun 2020 18:50:31: Fewer paired peaks (831) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 831 pairs to build model! INFO @ Sun, 21 Jun 2020 18:50:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:31: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 18:50:31: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 18:50:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.10_model.r INFO @ Sun, 21 Jun 2020 18:50:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:32: 7000000 INFO @ Sun, 21 Jun 2020 18:50:37: 8000000 INFO @ Sun, 21 Jun 2020 18:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.05_summits.bed INFO @ Sun, 21 Jun 2020 18:50:39: Done! pass1 - making usageList (587 chroms): 2 millis pass2 - checking and writing primary data (5323 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:50:42: 9000000 INFO @ Sun, 21 Jun 2020 18:50:48: 10000000 INFO @ Sun, 21 Jun 2020 18:50:53: 11000000 INFO @ Sun, 21 Jun 2020 18:50:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:59: 12000000 INFO @ Sun, 21 Jun 2020 18:51:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:51:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:51:00: #1 total tags in treatment: 12194775 INFO @ Sun, 21 Jun 2020 18:51:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:00: #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 18:51:00: #1 tags after filtering in treatment: 12194775 INFO @ Sun, 21 Jun 2020 18:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:01: #2 number of paired peaks: 831 WARNING @ Sun, 21 Jun 2020 18:51:01: Fewer paired peaks (831) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 831 pairs to build model! INFO @ Sun, 21 Jun 2020 18:51:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:02: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:02: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:02: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 18:51:02: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 18:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.20_model.r INFO @ Sun, 21 Jun 2020 18:51:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:51:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.10_summits.bed INFO @ Sun, 21 Jun 2020 18:51:11: Done! pass1 - making usageList (505 chroms): 1 millis pass2 - checking and writing primary data (2812 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:51:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618531/SRX2618531.20_summits.bed INFO @ Sun, 21 Jun 2020 18:51:41: Done! pass1 - making usageList (371 chroms): 2 millis pass2 - checking and writing primary data (1199 records, 4 fields): 13 millis CompletedMACS2peakCalling