Job ID = 14168346 SRX = SRX11078120 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T08:51:44 prefetch.2.10.7: 1) Downloading 'SRR14743548'... 2021-12-10T08:51:44 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T08:52:34 prefetch.2.10.7: HTTPS download succeed 2021-12-10T08:52:34 prefetch.2.10.7: 1) 'SRR14743548' was downloaded successfully 2021-12-10T08:52:34 prefetch.2.10.7: 'SRR14743548' has 0 unresolved dependencies Read 29747363 spots for SRR14743548/SRR14743548.sra Written 29747363 spots for SRR14743548/SRR14743548.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169503 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:19 29747363 reads; of these: 29747363 (100.00%) were paired; of these: 25492947 (85.70%) aligned concordantly 0 times 3288182 (11.05%) aligned concordantly exactly 1 time 966234 (3.25%) aligned concordantly >1 times ---- 25492947 pairs aligned concordantly 0 times; of these: 5744 (0.02%) aligned discordantly 1 time ---- 25487203 pairs aligned 0 times concordantly or discordantly; of these: 50974406 mates make up the pairs; of these: 50649790 (99.36%) aligned 0 times 155408 (0.30%) aligned exactly 1 time 169208 (0.33%) aligned >1 times 14.87% overall alignment rate Time searching: 00:08:20 Overall time: 00:08:20 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] 268994 / 4257641 = 0.0632 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 18:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.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 @ Fri, 10 Dec 2021 18:05:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:05:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:05:25: 1000000 INFO @ Fri, 10 Dec 2021 18:05:30: 2000000 INFO @ Fri, 10 Dec 2021 18:05:35: 3000000 INFO @ Fri, 10 Dec 2021 18:05:40: 4000000 INFO @ Fri, 10 Dec 2021 18:05:45: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 18:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.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 @ Fri, 10 Dec 2021 18:05:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:05:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:05:50: 6000000 INFO @ Fri, 10 Dec 2021 18:05:57: 7000000 INFO @ Fri, 10 Dec 2021 18:05:57: 1000000 INFO @ Fri, 10 Dec 2021 18:06:03: 8000000 INFO @ Fri, 10 Dec 2021 18:06:04: 2000000 INFO @ Fri, 10 Dec 2021 18:06:05: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:06:05: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:06:05: #1 total tags in treatment: 3985544 INFO @ Fri, 10 Dec 2021 18:06:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:06:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:06:05: #1 tags after filtering in treatment: 3738778 INFO @ Fri, 10 Dec 2021 18:06:05: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 18:06:05: #1 finished! INFO @ Fri, 10 Dec 2021 18:06:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:06:05: #2 number of paired peaks: 658 WARNING @ Fri, 10 Dec 2021 18:06:05: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 10 Dec 2021 18:06:05: start model_add_line... INFO @ Fri, 10 Dec 2021 18:06:06: start X-correlation... INFO @ Fri, 10 Dec 2021 18:06:06: end of X-cor INFO @ Fri, 10 Dec 2021 18:06:06: #2 finished! INFO @ Fri, 10 Dec 2021 18:06:06: #2 predicted fragment length is 114 bps INFO @ Fri, 10 Dec 2021 18:06:06: #2 alternative fragment length(s) may be 4,114 bps INFO @ Fri, 10 Dec 2021 18:06:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.05_model.r INFO @ Fri, 10 Dec 2021 18:06:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:06:11: 3000000 INFO @ Fri, 10 Dec 2021 18:06:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:06:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:06:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.05_summits.bed INFO @ Fri, 10 Dec 2021 18:06:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (396 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 18:06:18: 4000000 INFO @ Fri, 10 Dec 2021 18:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.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 @ Fri, 10 Dec 2021 18:06:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:06:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:06:25: 5000000 INFO @ Fri, 10 Dec 2021 18:06:27: 1000000 INFO @ Fri, 10 Dec 2021 18:06:33: 6000000 INFO @ Fri, 10 Dec 2021 18:06:34: 2000000 INFO @ Fri, 10 Dec 2021 18:06:40: 7000000 INFO @ Fri, 10 Dec 2021 18:06:42: 3000000 INFO @ Fri, 10 Dec 2021 18:06:47: 8000000 INFO @ Fri, 10 Dec 2021 18:06:49: 4000000 INFO @ Fri, 10 Dec 2021 18:06:49: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:06:49: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:06:49: #1 total tags in treatment: 3985544 INFO @ Fri, 10 Dec 2021 18:06:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:06:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:06:49: #1 tags after filtering in treatment: 3738778 INFO @ Fri, 10 Dec 2021 18:06:49: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 18:06:49: #1 finished! INFO @ Fri, 10 Dec 2021 18:06:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:06:50: #2 number of paired peaks: 658 WARNING @ Fri, 10 Dec 2021 18:06:50: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 10 Dec 2021 18:06:50: start model_add_line... INFO @ Fri, 10 Dec 2021 18:06:50: start X-correlation... INFO @ Fri, 10 Dec 2021 18:06:50: end of X-cor INFO @ Fri, 10 Dec 2021 18:06:50: #2 finished! INFO @ Fri, 10 Dec 2021 18:06:50: #2 predicted fragment length is 114 bps INFO @ Fri, 10 Dec 2021 18:06:50: #2 alternative fragment length(s) may be 4,114 bps INFO @ Fri, 10 Dec 2021 18:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.10_model.r INFO @ Fri, 10 Dec 2021 18:06:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:06:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:06:56: 5000000 INFO @ Fri, 10 Dec 2021 18:06:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:07:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:07:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:07:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.10_summits.bed INFO @ Fri, 10 Dec 2021 18:07:01: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:07:03: 6000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:07:10: 7000000 INFO @ Fri, 10 Dec 2021 18:07:16: 8000000 INFO @ Fri, 10 Dec 2021 18:07:18: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:07:18: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:07:18: #1 total tags in treatment: 3985544 INFO @ Fri, 10 Dec 2021 18:07:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:07:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:07:18: #1 tags after filtering in treatment: 3738778 INFO @ Fri, 10 Dec 2021 18:07:18: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 18:07:18: #1 finished! INFO @ Fri, 10 Dec 2021 18:07:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:07:19: #2 number of paired peaks: 658 WARNING @ Fri, 10 Dec 2021 18:07:19: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 10 Dec 2021 18:07:19: start model_add_line... INFO @ Fri, 10 Dec 2021 18:07:19: start X-correlation... INFO @ Fri, 10 Dec 2021 18:07:19: end of X-cor INFO @ Fri, 10 Dec 2021 18:07:19: #2 finished! INFO @ Fri, 10 Dec 2021 18:07:19: #2 predicted fragment length is 114 bps INFO @ Fri, 10 Dec 2021 18:07:19: #2 alternative fragment length(s) may be 4,114 bps INFO @ Fri, 10 Dec 2021 18:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.20_model.r INFO @ Fri, 10 Dec 2021 18:07:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:07:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:07:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:07:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:07:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078120/SRX11078120.20_summits.bed INFO @ Fri, 10 Dec 2021 18:07:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 1 millis CompletedMACS2peakCalling