Job ID = 16438696 SRX = SRX15206507 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:05:26 prefetch.2.10.7: 1) Downloading 'SRR19139285'... 2022-08-02T05:05:26 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:05:33 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:05:33 prefetch.2.10.7: 'SRR19139285' is valid 2022-08-02T05:05:33 prefetch.2.10.7: 1) 'SRR19139285' was downloaded successfully 2022-08-02T05:05:33 prefetch.2.10.7: 'SRR19139285' has 0 unresolved dependencies Read 2718303 spots for SRR19139285/SRR19139285.sra Written 2718303 spots for SRR19139285/SRR19139285.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438921 ("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: 00:01:27 2718303 reads; of these: 2718303 (100.00%) were unpaired; of these: 122945 (4.52%) aligned 0 times 1860495 (68.44%) aligned exactly 1 time 734863 (27.03%) aligned >1 times 95.48% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 309531 / 2595358 = 0.1193 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 14:08:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.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 14:08:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:08:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:08:27: 1000000 INFO @ Tue, 02 Aug 2022 14:08:32: 2000000 INFO @ Tue, 02 Aug 2022 14:08:34: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:08:34: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:08:34: #1 total tags in treatment: 2285827 INFO @ Tue, 02 Aug 2022 14:08:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:08:34: #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 14:08:34: #1 tags after filtering in treatment: 2285827 INFO @ Tue, 02 Aug 2022 14:08:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:08:34: #1 finished! INFO @ Tue, 02 Aug 2022 14:08:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:08:34: #2 number of paired peaks: 586 WARNING @ Tue, 02 Aug 2022 14:08:34: Fewer paired peaks (586) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 586 pairs to build model! INFO @ Tue, 02 Aug 2022 14:08:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:08:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:08:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:08:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:08:34: #2 predicted fragment length is 129 bps INFO @ Tue, 02 Aug 2022 14:08:34: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 02 Aug 2022 14:08:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.05_model.r WARNING @ Tue, 02 Aug 2022 14:08:34: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:08:34: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 02 Aug 2022 14:08:34: #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 14:08:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:08:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:08:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:08:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:08:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:08:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.05_summits.bed INFO @ Tue, 02 Aug 2022 14:08:42: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1564 records, 4 fields): 29 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 14:08:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.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 14:08:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:08:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:08:56: 1000000 INFO @ Tue, 02 Aug 2022 14:09:02: 2000000 INFO @ Tue, 02 Aug 2022 14:09:04: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:09:04: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:09:04: #1 total tags in treatment: 2285827 INFO @ Tue, 02 Aug 2022 14:09:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:09:04: #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 14:09:04: #1 tags after filtering in treatment: 2285827 INFO @ Tue, 02 Aug 2022 14:09:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:09:04: #1 finished! INFO @ Tue, 02 Aug 2022 14:09:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:09:04: #2 number of paired peaks: 586 WARNING @ Tue, 02 Aug 2022 14:09:04: Fewer paired peaks (586) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 586 pairs to build model! INFO @ Tue, 02 Aug 2022 14:09:04: start model_add_line... INFO @ Tue, 02 Aug 2022 14:09:04: start X-correlation... INFO @ Tue, 02 Aug 2022 14:09:04: end of X-cor INFO @ Tue, 02 Aug 2022 14:09:04: #2 finished! INFO @ Tue, 02 Aug 2022 14:09:04: #2 predicted fragment length is 129 bps INFO @ Tue, 02 Aug 2022 14:09:04: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 02 Aug 2022 14:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.10_model.r WARNING @ Tue, 02 Aug 2022 14:09:04: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:09:04: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 02 Aug 2022 14:09:04: #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 14:09:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:09:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.10_summits.bed INFO @ Tue, 02 Aug 2022 14:09:11: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 28 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 14:09:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.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 14:09:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:09:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:09:28: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:09:34: 2000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:09:36: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:09:36: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:09:36: #1 total tags in treatment: 2285827 INFO @ Tue, 02 Aug 2022 14:09:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:09:36: #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 14:09:36: #1 tags after filtering in treatment: 2285827 INFO @ Tue, 02 Aug 2022 14:09:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:09:36: #1 finished! INFO @ Tue, 02 Aug 2022 14:09:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:09:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:09:37: #2 number of paired peaks: 586 WARNING @ Tue, 02 Aug 2022 14:09:37: Fewer paired peaks (586) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 586 pairs to build model! INFO @ Tue, 02 Aug 2022 14:09:37: start model_add_line... INFO @ Tue, 02 Aug 2022 14:09:37: start X-correlation... INFO @ Tue, 02 Aug 2022 14:09:37: end of X-cor INFO @ Tue, 02 Aug 2022 14:09:37: #2 finished! INFO @ Tue, 02 Aug 2022 14:09:37: #2 predicted fragment length is 129 bps INFO @ Tue, 02 Aug 2022 14:09:37: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 02 Aug 2022 14:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.20_model.r WARNING @ Tue, 02 Aug 2022 14:09:37: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:09:37: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 02 Aug 2022 14:09:37: #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 14:09:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:09:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:09:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:09:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:09:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:09:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206507/SRX15206507.20_summits.bed INFO @ Tue, 02 Aug 2022 14:09:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 31 millis CompletedMACS2peakCalling