Job ID = 16438913 SRX = SRX15206515 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:08:40 prefetch.2.10.7: 1) Downloading 'SRR19139277'... 2022-08-02T05:08:40 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:09:02 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:09:03 prefetch.2.10.7: 'SRR19139277' is valid 2022-08-02T05:09:03 prefetch.2.10.7: 1) 'SRR19139277' was downloaded successfully 2022-08-02T05:09:03 prefetch.2.10.7: 'SRR19139277' has 0 unresolved dependencies Read 11743738 spots for SRR19139277/SRR19139277.sra Written 11743738 spots for SRR19139277/SRR19139277.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438971 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:55 11743738 reads; of these: 11743738 (100.00%) were unpaired; of these: 953185 (8.12%) aligned 0 times 9131263 (77.75%) aligned exactly 1 time 1659290 (14.13%) aligned >1 times 91.88% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8684249 / 10790553 = 0.8048 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 14:18:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.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 14:18:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:18:07: 1000000 INFO @ Tue, 02 Aug 2022 14:18:13: 2000000 INFO @ Tue, 02 Aug 2022 14:18:14: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:18:14: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:18:14: #1 total tags in treatment: 2106304 INFO @ Tue, 02 Aug 2022 14:18:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:14: #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 14:18:14: #1 tags after filtering in treatment: 2106304 INFO @ Tue, 02 Aug 2022 14:18:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:14: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:14: #2 number of paired peaks: 909 WARNING @ Tue, 02 Aug 2022 14:18:14: Fewer paired peaks (909) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 909 pairs to build model! INFO @ Tue, 02 Aug 2022 14:18:14: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:14: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:14: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:14: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:14: #2 predicted fragment length is 146 bps INFO @ Tue, 02 Aug 2022 14:18:14: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 02 Aug 2022 14:18:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.05_model.r WARNING @ Tue, 02 Aug 2022 14:18:14: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:14: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Tue, 02 Aug 2022 14:18:14: #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 14:18:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:18:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.05_summits.bed INFO @ Tue, 02 Aug 2022 14:18:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1069 records, 4 fields): 37 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 14:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.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 14:18:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:18:38: 1000000 INFO @ Tue, 02 Aug 2022 14:18:45: 2000000 INFO @ Tue, 02 Aug 2022 14:18:46: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:18:46: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:18:46: #1 total tags in treatment: 2106304 INFO @ Tue, 02 Aug 2022 14:18:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:46: #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 14:18:46: #1 tags after filtering in treatment: 2106304 INFO @ Tue, 02 Aug 2022 14:18:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:46: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:46: #2 number of paired peaks: 909 WARNING @ Tue, 02 Aug 2022 14:18:46: Fewer paired peaks (909) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 909 pairs to build model! INFO @ Tue, 02 Aug 2022 14:18:46: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:46: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:46: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:46: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:46: #2 predicted fragment length is 146 bps INFO @ Tue, 02 Aug 2022 14:18:46: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 02 Aug 2022 14:18:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.10_model.r WARNING @ Tue, 02 Aug 2022 14:18:46: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:46: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Tue, 02 Aug 2022 14:18:46: #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 14:18:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:18:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.10_summits.bed INFO @ Tue, 02 Aug 2022 14:18:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (226 records, 4 fields): 27 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 14:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.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 14:19:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:08: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:19:15: 2000000 INFO @ Tue, 02 Aug 2022 14:19:16: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:19:16: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:19:16: #1 total tags in treatment: 2106304 INFO @ Tue, 02 Aug 2022 14:19:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:19:16: #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 14:19:16: #1 tags after filtering in treatment: 2106304 INFO @ Tue, 02 Aug 2022 14:19:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:19:16: #1 finished! INFO @ Tue, 02 Aug 2022 14:19:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:19:16: #2 number of paired peaks: 909 WARNING @ Tue, 02 Aug 2022 14:19:16: Fewer paired peaks (909) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 909 pairs to build model! INFO @ Tue, 02 Aug 2022 14:19:16: start model_add_line... INFO @ Tue, 02 Aug 2022 14:19:16: start X-correlation... INFO @ Tue, 02 Aug 2022 14:19:16: end of X-cor INFO @ Tue, 02 Aug 2022 14:19:16: #2 finished! INFO @ Tue, 02 Aug 2022 14:19:16: #2 predicted fragment length is 146 bps INFO @ Tue, 02 Aug 2022 14:19:16: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 02 Aug 2022 14:19:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.20_model.r WARNING @ Tue, 02 Aug 2022 14:19:16: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:19:16: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Tue, 02 Aug 2022 14:19:16: #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 14:19:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:19:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:19:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:19:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:19:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:19:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206515/SRX15206515.20_summits.bed INFO @ Tue, 02 Aug 2022 14:19:23: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 66 millis CompletedMACS2peakCalling