Job ID = 6527958 SRX = SRX3434311 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T13:42:30 prefetch.2.10.7: 1) Downloading 'SRR6335193'... 2020-06-29T13:42:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:42:54 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:42:54 prefetch.2.10.7: 'SRR6335193' is valid 2020-06-29T13:42:54 prefetch.2.10.7: 1) 'SRR6335193' was downloaded successfully 2020-06-29T13:42:54 prefetch.2.10.7: 'SRR6335193' has 0 unresolved dependencies Read 535226 spots for SRR6335193/SRR6335193.sra Written 535226 spots for SRR6335193/SRR6335193.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: 00:00:48 535226 reads; of these: 535226 (100.00%) were paired; of these: 94998 (17.75%) aligned concordantly 0 times 392550 (73.34%) aligned concordantly exactly 1 time 47678 (8.91%) aligned concordantly >1 times ---- 94998 pairs aligned concordantly 0 times; of these: 42185 (44.41%) aligned discordantly 1 time ---- 52813 pairs aligned 0 times concordantly or discordantly; of these: 105626 mates make up the pairs; of these: 71868 (68.04%) aligned 0 times 21666 (20.51%) aligned exactly 1 time 12092 (11.45%) aligned >1 times 93.29% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 7464 / 411989 = 0.0181 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 @ Mon, 29 Jun 2020 22:45:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.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 @ Mon, 29 Jun 2020 22:45:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:45:14: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:45:21: #1 tag size is determined as 73 bps INFO @ Mon, 29 Jun 2020 22:45:21: #1 tag size = 73 INFO @ Mon, 29 Jun 2020 22:45:21: #1 total tags in treatment: 433712 INFO @ Mon, 29 Jun 2020 22:45:21: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:45:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:45:21: #1 tags after filtering in treatment: 430648 INFO @ Mon, 29 Jun 2020 22:45:21: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 29 Jun 2020 22:45:21: #1 finished! INFO @ Mon, 29 Jun 2020 22:45:21: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:45:21: #2 number of paired peaks: 379 WARNING @ Mon, 29 Jun 2020 22:45:21: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Mon, 29 Jun 2020 22:45:21: start model_add_line... INFO @ Mon, 29 Jun 2020 22:45:21: start X-correlation... INFO @ Mon, 29 Jun 2020 22:45:21: end of X-cor INFO @ Mon, 29 Jun 2020 22:45:21: #2 finished! INFO @ Mon, 29 Jun 2020 22:45:21: #2 predicted fragment length is 211 bps INFO @ Mon, 29 Jun 2020 22:45:21: #2 alternative fragment length(s) may be 116,130,179,211,264,290 bps INFO @ Mon, 29 Jun 2020 22:45:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.05_model.r INFO @ Mon, 29 Jun 2020 22:45:21: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:45:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:45:22: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.05_summits.bed INFO @ Mon, 29 Jun 2020 22:45:23: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Mon, 29 Jun 2020 22:45:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.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 @ Mon, 29 Jun 2020 22:45:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:45:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:45:51: #1 tag size is determined as 73 bps INFO @ Mon, 29 Jun 2020 22:45:51: #1 tag size = 73 INFO @ Mon, 29 Jun 2020 22:45:51: #1 total tags in treatment: 433712 INFO @ Mon, 29 Jun 2020 22:45:51: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:45:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:45:51: #1 tags after filtering in treatment: 430648 INFO @ Mon, 29 Jun 2020 22:45:51: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 29 Jun 2020 22:45:51: #1 finished! INFO @ Mon, 29 Jun 2020 22:45:51: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:45:51: #2 number of paired peaks: 379 WARNING @ Mon, 29 Jun 2020 22:45:51: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Mon, 29 Jun 2020 22:45:51: start model_add_line... INFO @ Mon, 29 Jun 2020 22:45:51: start X-correlation... INFO @ Mon, 29 Jun 2020 22:45:51: end of X-cor INFO @ Mon, 29 Jun 2020 22:45:51: #2 finished! INFO @ Mon, 29 Jun 2020 22:45:51: #2 predicted fragment length is 211 bps INFO @ Mon, 29 Jun 2020 22:45:51: #2 alternative fragment length(s) may be 116,130,179,211,264,290 bps INFO @ Mon, 29 Jun 2020 22:45:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.10_model.r INFO @ Mon, 29 Jun 2020 22:45:51: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:45:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:45:52: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:45:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:45:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:45:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.10_summits.bed INFO @ Mon, 29 Jun 2020 22:45:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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 @ Mon, 29 Jun 2020 22:46:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.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 @ Mon, 29 Jun 2020 22:46:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:46:14: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:46:22: #1 tag size is determined as 73 bps INFO @ Mon, 29 Jun 2020 22:46:22: #1 tag size = 73 INFO @ Mon, 29 Jun 2020 22:46:22: #1 total tags in treatment: 433712 INFO @ Mon, 29 Jun 2020 22:46:22: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:46:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:46:22: #1 tags after filtering in treatment: 430648 INFO @ Mon, 29 Jun 2020 22:46:22: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 29 Jun 2020 22:46:22: #1 finished! INFO @ Mon, 29 Jun 2020 22:46:22: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:46:22: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:46:22: #2 number of paired peaks: 379 WARNING @ Mon, 29 Jun 2020 22:46:22: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Mon, 29 Jun 2020 22:46:22: start model_add_line... INFO @ Mon, 29 Jun 2020 22:46:22: start X-correlation... INFO @ Mon, 29 Jun 2020 22:46:22: end of X-cor INFO @ Mon, 29 Jun 2020 22:46:22: #2 finished! INFO @ Mon, 29 Jun 2020 22:46:22: #2 predicted fragment length is 211 bps INFO @ Mon, 29 Jun 2020 22:46:22: #2 alternative fragment length(s) may be 116,130,179,211,264,290 bps INFO @ Mon, 29 Jun 2020 22:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.20_model.r INFO @ Mon, 29 Jun 2020 22:46:22: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:46:23: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434311/SRX3434311.20_summits.bed INFO @ Mon, 29 Jun 2020 22:46:23: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling