Job ID = 16438948 SRX = SRX15206523 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:14:08 prefetch.2.10.7: 1) Downloading 'SRR19139269'... 2022-08-02T05:14:08 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:14:15 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:14:16 prefetch.2.10.7: 'SRR19139269' is valid 2022-08-02T05:14:16 prefetch.2.10.7: 1) 'SRR19139269' was downloaded successfully 2022-08-02T05:14:16 prefetch.2.10.7: 'SRR19139269' has 0 unresolved dependencies Read 3207150 spots for SRR19139269/SRR19139269.sra Written 3207150 spots for SRR19139269/SRR19139269.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438975 ("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: 00:01:35 3207150 reads; of these: 3207150 (100.00%) were unpaired; of these: 188953 (5.89%) aligned 0 times 2171771 (67.72%) aligned exactly 1 time 846426 (26.39%) aligned >1 times 94.11% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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] 655384 / 3018197 = 0.2171 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 14:17:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.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 14:17:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:17:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:17:30: 1000000 INFO @ Tue, 02 Aug 2022 14:17:38: 2000000 INFO @ Tue, 02 Aug 2022 14:17:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:17:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:17:40: #1 total tags in treatment: 2362813 INFO @ Tue, 02 Aug 2022 14:17:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:17:40: #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 14:17:40: #1 tags after filtering in treatment: 2362813 INFO @ Tue, 02 Aug 2022 14:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:17:40: #1 finished! INFO @ Tue, 02 Aug 2022 14:17:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:17:41: #2 number of paired peaks: 559 WARNING @ Tue, 02 Aug 2022 14:17:41: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 02 Aug 2022 14:17:41: start model_add_line... INFO @ Tue, 02 Aug 2022 14:17:41: start X-correlation... INFO @ Tue, 02 Aug 2022 14:17:41: end of X-cor INFO @ Tue, 02 Aug 2022 14:17:41: #2 finished! INFO @ Tue, 02 Aug 2022 14:17:41: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 14:17:41: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 02 Aug 2022 14:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.05_model.r WARNING @ Tue, 02 Aug 2022 14:17:41: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:17:41: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 02 Aug 2022 14:17:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:17:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:17:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:17:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:17:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:17:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.05_summits.bed INFO @ Tue, 02 Aug 2022 14:17:49: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (732 records, 4 fields): 23 millis CompletedMACS2peakCalling 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 14:17:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.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 14:17:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:17:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:17:59: 1000000 INFO @ Tue, 02 Aug 2022 14:18:07: 2000000 INFO @ Tue, 02 Aug 2022 14:18:10: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:18:10: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:18:10: #1 total tags in treatment: 2362813 INFO @ Tue, 02 Aug 2022 14:18:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:10: #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 14:18:10: #1 tags after filtering in treatment: 2362813 INFO @ Tue, 02 Aug 2022 14:18:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:10: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:10: #2 number of paired peaks: 559 WARNING @ Tue, 02 Aug 2022 14:18:10: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 02 Aug 2022 14:18:10: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:10: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:10: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:10: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:10: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 14:18:10: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 02 Aug 2022 14:18:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.10_model.r WARNING @ Tue, 02 Aug 2022 14:18:10: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:10: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 02 Aug 2022 14:18:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:18:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:18:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.10_summits.bed INFO @ Tue, 02 Aug 2022 14:18:18: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (325 records, 4 fields): 16 millis CompletedMACS2peakCalling 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 14:18:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.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 14:18:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:18:29: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:18:37: 2000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:18:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:18:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:18:40: #1 total tags in treatment: 2362813 INFO @ Tue, 02 Aug 2022 14:18:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:40: #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 14:18:40: #1 tags after filtering in treatment: 2362813 INFO @ Tue, 02 Aug 2022 14:18:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:40: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:40: #2 number of paired peaks: 559 WARNING @ Tue, 02 Aug 2022 14:18:40: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 02 Aug 2022 14:18:40: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:40: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:40: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:40: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:40: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 14:18:40: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 02 Aug 2022 14:18:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.20_model.r WARNING @ Tue, 02 Aug 2022 14:18:40: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:40: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 02 Aug 2022 14:18:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:18:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:18:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206523/SRX15206523.20_summits.bed INFO @ Tue, 02 Aug 2022 14:18:48: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 26 millis CompletedMACS2peakCalling