Job ID = 16439192 SRX = SRX15206469 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:45:31 prefetch.2.10.7: 1) Downloading 'SRR19139337'... 2022-08-02T05:45:31 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:45:40 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:45:40 prefetch.2.10.7: 'SRR19139337' is valid 2022-08-02T05:45:40 prefetch.2.10.7: 1) 'SRR19139337' was downloaded successfully 2022-08-02T05:45:40 prefetch.2.10.7: 'SRR19139337' has 0 unresolved dependencies Read 4414203 spots for SRR19139337/SRR19139337.sra Written 4414203 spots for SRR19139337/SRR19139337.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439288 ("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: 00:02:25 4414203 reads; of these: 4414203 (100.00%) were unpaired; of these: 54484 (1.23%) aligned 0 times 1805408 (40.90%) aligned exactly 1 time 2554311 (57.87%) aligned >1 times 98.77% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 252223 / 4359719 = 0.0579 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 14:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.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 14:49:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:01: 1000000 INFO @ Tue, 02 Aug 2022 14:50:06: 2000000 INFO @ Tue, 02 Aug 2022 14:50:11: 3000000 INFO @ Tue, 02 Aug 2022 14:50:16: 4000000 INFO @ Tue, 02 Aug 2022 14:50:17: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:50:17: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:50:17: #1 total tags in treatment: 4107496 INFO @ Tue, 02 Aug 2022 14:50:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:17: #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 14:50:17: #1 tags after filtering in treatment: 4107496 INFO @ Tue, 02 Aug 2022 14:50:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:17: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:17: #2 number of paired peaks: 772 WARNING @ Tue, 02 Aug 2022 14:50:17: Fewer paired peaks (772) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 772 pairs to build model! INFO @ Tue, 02 Aug 2022 14:50:17: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:17: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:17: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:17: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:17: #2 predicted fragment length is 87 bps INFO @ Tue, 02 Aug 2022 14:50:17: #2 alternative fragment length(s) may be 87,597 bps INFO @ Tue, 02 Aug 2022 14:50:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.05_model.r WARNING @ Tue, 02 Aug 2022 14:50:17: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:50:17: #2 You may need to consider one of the other alternative d(s): 87,597 WARNING @ Tue, 02 Aug 2022 14:50:17: #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 14:50:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:17: #3 Pre-compute pvalue-qvalue table... 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 14:50:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.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 14:50:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.05_summits.bed INFO @ Tue, 02 Aug 2022 14:50:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1205 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:32: 1000000 INFO @ Tue, 02 Aug 2022 14:50:38: 2000000 INFO @ Tue, 02 Aug 2022 14:50:44: 3000000 INFO @ Tue, 02 Aug 2022 14:50:49: 4000000 INFO @ Tue, 02 Aug 2022 14:50:50: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:50:50: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:50:50: #1 total tags in treatment: 4107496 INFO @ Tue, 02 Aug 2022 14:50:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:50: #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 14:50:50: #1 tags after filtering in treatment: 4107496 INFO @ Tue, 02 Aug 2022 14:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:50: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:50: #2 number of paired peaks: 772 WARNING @ Tue, 02 Aug 2022 14:50:50: Fewer paired peaks (772) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 772 pairs to build model! INFO @ Tue, 02 Aug 2022 14:50:50: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:50: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:50: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:50: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:50: #2 predicted fragment length is 87 bps INFO @ Tue, 02 Aug 2022 14:50:50: #2 alternative fragment length(s) may be 87,597 bps INFO @ Tue, 02 Aug 2022 14:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.10_model.r WARNING @ Tue, 02 Aug 2022 14:50:50: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:50:50: #2 You may need to consider one of the other alternative d(s): 87,597 WARNING @ Tue, 02 Aug 2022 14:50:50: #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 14:50:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:50: #3 Pre-compute pvalue-qvalue table... 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 14:50:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.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 14:50:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:02: 1000000 INFO @ Tue, 02 Aug 2022 14:51:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.10_summits.bed INFO @ Tue, 02 Aug 2022 14:51:04: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (376 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:51:08: 2000000 INFO @ Tue, 02 Aug 2022 14:51:13: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:51:19: 4000000 INFO @ Tue, 02 Aug 2022 14:51:20: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:51:20: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:51:20: #1 total tags in treatment: 4107496 INFO @ Tue, 02 Aug 2022 14:51:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:51:20: #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 14:51:20: #1 tags after filtering in treatment: 4107496 INFO @ Tue, 02 Aug 2022 14:51:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:51:20: #1 finished! INFO @ Tue, 02 Aug 2022 14:51:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:51:20: #2 number of paired peaks: 772 WARNING @ Tue, 02 Aug 2022 14:51:20: Fewer paired peaks (772) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 772 pairs to build model! INFO @ Tue, 02 Aug 2022 14:51:20: start model_add_line... INFO @ Tue, 02 Aug 2022 14:51:20: start X-correlation... INFO @ Tue, 02 Aug 2022 14:51:20: end of X-cor INFO @ Tue, 02 Aug 2022 14:51:20: #2 finished! INFO @ Tue, 02 Aug 2022 14:51:20: #2 predicted fragment length is 87 bps INFO @ Tue, 02 Aug 2022 14:51:20: #2 alternative fragment length(s) may be 87,597 bps INFO @ Tue, 02 Aug 2022 14:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.20_model.r WARNING @ Tue, 02 Aug 2022 14:51:20: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:51:20: #2 You may need to consider one of the other alternative d(s): 87,597 WARNING @ Tue, 02 Aug 2022 14:51:20: #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 14:51:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:51:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:51:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206469/SRX15206469.20_summits.bed INFO @ Tue, 02 Aug 2022 14:51:34: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (103 records, 4 fields): 20 millis CompletedMACS2peakCalling