Job ID = 16438689 SRX = SRX15206502 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:03:39 prefetch.2.10.7: 1) Downloading 'SRR19139290'... 2022-08-02T05:03:39 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:03:52 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:03:53 prefetch.2.10.7: 'SRR19139290' is valid 2022-08-02T05:03:53 prefetch.2.10.7: 1) 'SRR19139290' was downloaded successfully 2022-08-02T05:03:53 prefetch.2.10.7: 'SRR19139290' has 0 unresolved dependencies Read 10039443 spots for SRR19139290/SRR19139290.sra Written 10039443 spots for SRR19139290/SRR19139290.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438925 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:01 10039443 reads; of these: 10039443 (100.00%) were unpaired; of these: 374759 (3.73%) aligned 0 times 8249660 (82.17%) aligned exactly 1 time 1415024 (14.09%) aligned >1 times 96.27% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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_rmdupse_core] 457006 / 9664684 = 0.0473 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.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, 02 Aug 2022 14:10:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:10:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:11:02: 1000000 INFO @ Tue, 02 Aug 2022 14:11:10: 2000000 INFO @ Tue, 02 Aug 2022 14:11:18: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.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, 02 Aug 2022 14:11:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:11:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:11:26: 4000000 INFO @ Tue, 02 Aug 2022 14:11:31: 1000000 INFO @ Tue, 02 Aug 2022 14:11:34: 5000000 INFO @ Tue, 02 Aug 2022 14:11:38: 2000000 INFO @ Tue, 02 Aug 2022 14:11:42: 6000000 INFO @ Tue, 02 Aug 2022 14:11:45: 3000000 INFO @ Tue, 02 Aug 2022 14:11:50: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:11:53: 4000000 INFO @ Tue, 02 Aug 2022 14:11:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.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, 02 Aug 2022 14:11:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:11:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:11:58: 8000000 INFO @ Tue, 02 Aug 2022 14:12:01: 5000000 INFO @ Tue, 02 Aug 2022 14:12:04: 1000000 INFO @ Tue, 02 Aug 2022 14:12:06: 9000000 INFO @ Tue, 02 Aug 2022 14:12:08: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:12:08: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:12:08: #1 total tags in treatment: 9207678 INFO @ Tue, 02 Aug 2022 14:12:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:12:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:12:08: #1 tags after filtering in treatment: 9207678 INFO @ Tue, 02 Aug 2022 14:12:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:12:08: #1 finished! INFO @ Tue, 02 Aug 2022 14:12:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:12:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:12:09: #2 number of paired peaks: 119 WARNING @ Tue, 02 Aug 2022 14:12:09: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 02 Aug 2022 14:12:09: start model_add_line... INFO @ Tue, 02 Aug 2022 14:12:09: start X-correlation... INFO @ Tue, 02 Aug 2022 14:12:09: 6000000 INFO @ Tue, 02 Aug 2022 14:12:09: end of X-cor INFO @ Tue, 02 Aug 2022 14:12:09: #2 finished! INFO @ Tue, 02 Aug 2022 14:12:09: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 14:12:09: #2 alternative fragment length(s) may be 4,56,74,183,232,251,286 bps INFO @ Tue, 02 Aug 2022 14:12:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.05_model.r INFO @ Tue, 02 Aug 2022 14:12:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:12:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:12:11: 2000000 INFO @ Tue, 02 Aug 2022 14:12:17: 7000000 INFO @ Tue, 02 Aug 2022 14:12:19: 3000000 INFO @ Tue, 02 Aug 2022 14:12:25: 8000000 INFO @ Tue, 02 Aug 2022 14:12:27: 4000000 INFO @ Tue, 02 Aug 2022 14:12:33: 9000000 INFO @ Tue, 02 Aug 2022 14:12:34: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:12:34: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:12:34: #1 total tags in treatment: 9207678 INFO @ Tue, 02 Aug 2022 14:12:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:12:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:12:35: #1 tags after filtering in treatment: 9207678 INFO @ Tue, 02 Aug 2022 14:12:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:12:35: #1 finished! INFO @ Tue, 02 Aug 2022 14:12:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:12:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:12:35: 5000000 INFO @ Tue, 02 Aug 2022 14:12:35: #2 number of paired peaks: 119 WARNING @ Tue, 02 Aug 2022 14:12:35: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 02 Aug 2022 14:12:35: start model_add_line... INFO @ Tue, 02 Aug 2022 14:12:35: start X-correlation... INFO @ Tue, 02 Aug 2022 14:12:35: end of X-cor INFO @ Tue, 02 Aug 2022 14:12:35: #2 finished! INFO @ Tue, 02 Aug 2022 14:12:35: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 14:12:35: #2 alternative fragment length(s) may be 4,56,74,183,232,251,286 bps INFO @ Tue, 02 Aug 2022 14:12:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.10_model.r INFO @ Tue, 02 Aug 2022 14:12:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:12:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:12:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:12:42: 6000000 INFO @ Tue, 02 Aug 2022 14:12:49: 7000000 INFO @ Tue, 02 Aug 2022 14:12:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:12:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:12:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.05_summits.bed INFO @ Tue, 02 Aug 2022 14:12:51: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (93 records, 4 fields): 70 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:12:56: 8000000 INFO @ Tue, 02 Aug 2022 14:13:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:13:03: 9000000 INFO @ Tue, 02 Aug 2022 14:13:05: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:13:05: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:13:05: #1 total tags in treatment: 9207678 INFO @ Tue, 02 Aug 2022 14:13:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:13:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:13:05: #1 tags after filtering in treatment: 9207678 INFO @ Tue, 02 Aug 2022 14:13:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:13:05: #1 finished! INFO @ Tue, 02 Aug 2022 14:13:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:13:06: #2 number of paired peaks: 119 WARNING @ Tue, 02 Aug 2022 14:13:06: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 02 Aug 2022 14:13:06: start model_add_line... INFO @ Tue, 02 Aug 2022 14:13:06: start X-correlation... INFO @ Tue, 02 Aug 2022 14:13:06: end of X-cor INFO @ Tue, 02 Aug 2022 14:13:06: #2 finished! INFO @ Tue, 02 Aug 2022 14:13:06: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 14:13:06: #2 alternative fragment length(s) may be 4,56,74,183,232,251,286 bps INFO @ Tue, 02 Aug 2022 14:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.20_model.r INFO @ Tue, 02 Aug 2022 14:13:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.10_summits.bed INFO @ Tue, 02 Aug 2022 14:13:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:13:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:13:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:13:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:13:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206502/SRX15206502.20_summits.bed INFO @ Tue, 02 Aug 2022 14:13:47: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 24 millis CompletedMACS2peakCalling