Job ID = 16438691 SRX = SRX15206504 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:04:26 prefetch.2.10.7: 1) Downloading 'SRR19139288'... 2022-08-02T05:04:26 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:04:39 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:04:39 prefetch.2.10.7: 'SRR19139288' is valid 2022-08-02T05:04:39 prefetch.2.10.7: 1) 'SRR19139288' was downloaded successfully 2022-08-02T05:04:39 prefetch.2.10.7: 'SRR19139288' has 0 unresolved dependencies Read 6228842 spots for SRR19139288/SRR19139288.sra Written 6228842 spots for SRR19139288/SRR19139288.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438920 ("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: 00:02:06 6228842 reads; of these: 6228842 (100.00%) were unpaired; of these: 209719 (3.37%) aligned 0 times 5040496 (80.92%) aligned exactly 1 time 978627 (15.71%) aligned >1 times 96.63% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 231847 / 6019123 = 0.0385 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 14:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.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 14:09:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:09:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:09:16: 1000000 INFO @ Tue, 02 Aug 2022 14:09:24: 2000000 INFO @ Tue, 02 Aug 2022 14:09:30: 3000000 INFO @ Tue, 02 Aug 2022 14:09:36: 4000000 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 14:09:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.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 14:09:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:09:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:09:43: 5000000 INFO @ Tue, 02 Aug 2022 14:09:45: 1000000 INFO @ Tue, 02 Aug 2022 14:09:48: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:09:48: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:09:48: #1 total tags in treatment: 5787276 INFO @ Tue, 02 Aug 2022 14:09:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:09:48: #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 14:09:48: #1 tags after filtering in treatment: 5787276 INFO @ Tue, 02 Aug 2022 14:09:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:09:48: #1 finished! INFO @ Tue, 02 Aug 2022 14:09:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:09:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:09:48: #2 number of paired peaks: 146 WARNING @ Tue, 02 Aug 2022 14:09:48: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 02 Aug 2022 14:09:48: start model_add_line... INFO @ Tue, 02 Aug 2022 14:09:48: start X-correlation... INFO @ Tue, 02 Aug 2022 14:09:48: end of X-cor INFO @ Tue, 02 Aug 2022 14:09:48: #2 finished! INFO @ Tue, 02 Aug 2022 14:09:48: #2 predicted fragment length is 83 bps INFO @ Tue, 02 Aug 2022 14:09:48: #2 alternative fragment length(s) may be 3,83 bps INFO @ Tue, 02 Aug 2022 14:09:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.05_model.r WARNING @ Tue, 02 Aug 2022 14:09:48: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:09:48: #2 You may need to consider one of the other alternative d(s): 3,83 WARNING @ Tue, 02 Aug 2022 14:09:48: #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 14:09:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:09:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:09:52: 2000000 INFO @ Tue, 02 Aug 2022 14:09:57: 3000000 INFO @ Tue, 02 Aug 2022 14:10:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:10:03: 4000000 INFO @ Tue, 02 Aug 2022 14:10:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:10:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:10:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.05_summits.bed INFO @ Tue, 02 Aug 2022 14:10:07: Done! 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 14:10:09: 5000000 pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (105 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:10:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.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 14:10:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:10:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:10:13: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:10:13: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:10:13: #1 total tags in treatment: 5787276 INFO @ Tue, 02 Aug 2022 14:10:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:10:13: #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 14:10:13: #1 tags after filtering in treatment: 5787276 INFO @ Tue, 02 Aug 2022 14:10:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:10:13: #1 finished! INFO @ Tue, 02 Aug 2022 14:10:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:10:14: #2 number of paired peaks: 146 WARNING @ Tue, 02 Aug 2022 14:10:14: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 02 Aug 2022 14:10:14: start model_add_line... INFO @ Tue, 02 Aug 2022 14:10:14: start X-correlation... INFO @ Tue, 02 Aug 2022 14:10:14: end of X-cor INFO @ Tue, 02 Aug 2022 14:10:14: #2 finished! INFO @ Tue, 02 Aug 2022 14:10:14: #2 predicted fragment length is 83 bps INFO @ Tue, 02 Aug 2022 14:10:14: #2 alternative fragment length(s) may be 3,83 bps INFO @ Tue, 02 Aug 2022 14:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.10_model.r WARNING @ Tue, 02 Aug 2022 14:10:14: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:10:14: #2 You may need to consider one of the other alternative d(s): 3,83 WARNING @ Tue, 02 Aug 2022 14:10:14: #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 14:10:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:10:15: 1000000 INFO @ Tue, 02 Aug 2022 14:10:21: 2000000 INFO @ Tue, 02 Aug 2022 14:10:26: 3000000 INFO @ Tue, 02 Aug 2022 14:10:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:10:32: 4000000 INFO @ Tue, 02 Aug 2022 14:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.10_summits.bed INFO @ Tue, 02 Aug 2022 14:10:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (70 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:10:37: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:10:41: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:10:41: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:10:41: #1 total tags in treatment: 5787276 INFO @ Tue, 02 Aug 2022 14:10:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:10:41: #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 14:10:41: #1 tags after filtering in treatment: 5787276 INFO @ Tue, 02 Aug 2022 14:10:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:10:41: #1 finished! INFO @ Tue, 02 Aug 2022 14:10:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:10:42: #2 number of paired peaks: 146 WARNING @ Tue, 02 Aug 2022 14:10:42: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 02 Aug 2022 14:10:42: start model_add_line... INFO @ Tue, 02 Aug 2022 14:10:42: start X-correlation... INFO @ Tue, 02 Aug 2022 14:10:42: end of X-cor INFO @ Tue, 02 Aug 2022 14:10:42: #2 finished! INFO @ Tue, 02 Aug 2022 14:10:42: #2 predicted fragment length is 83 bps INFO @ Tue, 02 Aug 2022 14:10:42: #2 alternative fragment length(s) may be 3,83 bps INFO @ Tue, 02 Aug 2022 14:10:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.20_model.r WARNING @ Tue, 02 Aug 2022 14:10:42: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:10:42: #2 You may need to consider one of the other alternative d(s): 3,83 WARNING @ Tue, 02 Aug 2022 14:10:42: #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 14:10:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:10:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:10:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:11:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:11:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:11:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206504/SRX15206504.20_summits.bed INFO @ Tue, 02 Aug 2022 14:11:01: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 31 millis CompletedMACS2peakCalling