Job ID = 6529847 SRX = SRX5243665 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:24 9791909 reads; of these: 9791909 (100.00%) were unpaired; of these: 330876 (3.38%) aligned 0 times 7330777 (74.87%) aligned exactly 1 time 2130256 (21.76%) aligned >1 times 96.62% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 1922934 / 9461033 = 0.2032 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, 30 Jun 2020 02:52:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.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 @ Tue, 30 Jun 2020 02:52:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:26: 1000000 INFO @ Tue, 30 Jun 2020 02:52:32: 2000000 INFO @ Tue, 30 Jun 2020 02:52:37: 3000000 INFO @ Tue, 30 Jun 2020 02:52:43: 4000000 INFO @ Tue, 30 Jun 2020 02:52:48: 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, 30 Jun 2020 02:52:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.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 @ Tue, 30 Jun 2020 02:52:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:54: 6000000 INFO @ Tue, 30 Jun 2020 02:52:57: 1000000 INFO @ Tue, 30 Jun 2020 02:53:00: 7000000 INFO @ Tue, 30 Jun 2020 02:53:02: 2000000 INFO @ Tue, 30 Jun 2020 02:53:03: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:53:03: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:53:03: #1 total tags in treatment: 7538099 INFO @ Tue, 30 Jun 2020 02:53:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:53:03: #1 tags after filtering in treatment: 7537969 INFO @ Tue, 30 Jun 2020 02:53:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:03: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:04: #2 number of paired peaks: 318 WARNING @ Tue, 30 Jun 2020 02:53:04: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:04: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:04: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:04: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:04: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:04: #2 predicted fragment length is 209 bps INFO @ Tue, 30 Jun 2020 02:53:04: #2 alternative fragment length(s) may be 209 bps INFO @ Tue, 30 Jun 2020 02:53:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.05_model.r INFO @ Tue, 30 Jun 2020 02:53:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:08: 3000000 INFO @ Tue, 30 Jun 2020 02:53:13: 4000000 INFO @ Tue, 30 Jun 2020 02:53:19: 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, 30 Jun 2020 02:53:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.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 @ Tue, 30 Jun 2020 02:53:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:24: 6000000 INFO @ Tue, 30 Jun 2020 02:53:27: 1000000 INFO @ Tue, 30 Jun 2020 02:53:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.05_summits.bed INFO @ Tue, 30 Jun 2020 02:53:27: Done! pass1 - making usageList (390 chroms): 1 millis pass2 - checking and writing primary data (1762 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:30: 7000000 INFO @ Tue, 30 Jun 2020 02:53:33: 2000000 INFO @ Tue, 30 Jun 2020 02:53:34: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:53:34: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:53:34: #1 total tags in treatment: 7538099 INFO @ Tue, 30 Jun 2020 02:53:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:53:34: #1 tags after filtering in treatment: 7537969 INFO @ Tue, 30 Jun 2020 02:53:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:35: #2 number of paired peaks: 318 WARNING @ Tue, 30 Jun 2020 02:53:35: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:35: #2 predicted fragment length is 209 bps INFO @ Tue, 30 Jun 2020 02:53:35: #2 alternative fragment length(s) may be 209 bps INFO @ Tue, 30 Jun 2020 02:53:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.10_model.r INFO @ Tue, 30 Jun 2020 02:53:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:38: 3000000 INFO @ Tue, 30 Jun 2020 02:53:44: 4000000 INFO @ Tue, 30 Jun 2020 02:53:49: 5000000 INFO @ Tue, 30 Jun 2020 02:53:51: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:53:55: 6000000 INFO @ Tue, 30 Jun 2020 02:53:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.10_summits.bed INFO @ Tue, 30 Jun 2020 02:53:58: Done! pass1 - making usageList (265 chroms): 0 millis pass2 - checking and writing primary data (573 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:54:00: 7000000 INFO @ Tue, 30 Jun 2020 02:54:04: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:54:04: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:54:04: #1 total tags in treatment: 7538099 INFO @ Tue, 30 Jun 2020 02:54:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:54:04: #1 tags after filtering in treatment: 7537969 INFO @ Tue, 30 Jun 2020 02:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:04: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:04: #2 number of paired peaks: 318 WARNING @ Tue, 30 Jun 2020 02:54:04: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:04: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:04: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:04: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:04: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:04: #2 predicted fragment length is 209 bps INFO @ Tue, 30 Jun 2020 02:54:04: #2 alternative fragment length(s) may be 209 bps INFO @ Tue, 30 Jun 2020 02:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.20_model.r INFO @ Tue, 30 Jun 2020 02:54:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:54:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243665/SRX5243665.20_summits.bed INFO @ Tue, 30 Jun 2020 02:54:28: Done! pass1 - making usageList (152 chroms): 0 millis pass2 - checking and writing primary data (224 records, 4 fields): 11 millis CompletedMACS2peakCalling