Job ID = 16438947 SRX = SRX15206522 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:13:53 prefetch.2.10.7: 1) Downloading 'SRR19139270'... 2022-08-02T05:13:53 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:14:17 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:14:18 prefetch.2.10.7: 'SRR19139270' is valid 2022-08-02T05:14:18 prefetch.2.10.7: 1) 'SRR19139270' was downloaded successfully 2022-08-02T05:14:18 prefetch.2.10.7: 'SRR19139270' has 0 unresolved dependencies Read 14805375 spots for SRR19139270/SRR19139270.sra Written 14805375 spots for SRR19139270/SRR19139270.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439004 ("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: 00:05:11 14805375 reads; of these: 14805375 (100.00%) were unpaired; of these: 439177 (2.97%) aligned 0 times 11113287 (75.06%) aligned exactly 1 time 3252911 (21.97%) aligned >1 times 97.03% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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] 5328962 / 14366198 = 0.3709 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 14:23:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.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 14:23:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:23:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:23:37: 1000000 INFO @ Tue, 02 Aug 2022 14:23:42: 2000000 INFO @ Tue, 02 Aug 2022 14:23:47: 3000000 INFO @ Tue, 02 Aug 2022 14:23:52: 4000000 INFO @ Tue, 02 Aug 2022 14:23:56: 5000000 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 14:24:01: 6000000 INFO @ Tue, 02 Aug 2022 14:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.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 14:24:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:24:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:24:06: 7000000 INFO @ Tue, 02 Aug 2022 14:24:07: 1000000 INFO @ Tue, 02 Aug 2022 14:24:11: 8000000 INFO @ Tue, 02 Aug 2022 14:24:12: 2000000 INFO @ Tue, 02 Aug 2022 14:24:16: 9000000 INFO @ Tue, 02 Aug 2022 14:24:16: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:24:16: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:24:16: #1 total tags in treatment: 9037236 INFO @ Tue, 02 Aug 2022 14:24:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:24:16: #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 14:24:16: #1 tags after filtering in treatment: 9037236 INFO @ Tue, 02 Aug 2022 14:24:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:24:16: #1 finished! INFO @ Tue, 02 Aug 2022 14:24:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:24:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:24:17: 3000000 INFO @ Tue, 02 Aug 2022 14:24:17: #2 number of paired peaks: 786 WARNING @ Tue, 02 Aug 2022 14:24:17: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Tue, 02 Aug 2022 14:24:17: start model_add_line... INFO @ Tue, 02 Aug 2022 14:24:17: start X-correlation... INFO @ Tue, 02 Aug 2022 14:24:17: end of X-cor INFO @ Tue, 02 Aug 2022 14:24:17: #2 finished! INFO @ Tue, 02 Aug 2022 14:24:17: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 14:24:17: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 02 Aug 2022 14:24:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.05_model.r WARNING @ Tue, 02 Aug 2022 14:24:17: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:24:17: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 02 Aug 2022 14:24:17: #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 14:24:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:24:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:24:22: 4000000 INFO @ Tue, 02 Aug 2022 14:24:27: 5000000 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 14:24:32: 6000000 INFO @ Tue, 02 Aug 2022 14:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.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 14:24:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:24:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:24:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:24:37: 7000000 INFO @ Tue, 02 Aug 2022 14:24:37: 1000000 INFO @ Tue, 02 Aug 2022 14:24:42: 8000000 INFO @ Tue, 02 Aug 2022 14:24:42: 2000000 INFO @ Tue, 02 Aug 2022 14:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.05_summits.bed INFO @ Tue, 02 Aug 2022 14:24:46: Done! INFO @ Tue, 02 Aug 2022 14:24:47: 9000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4206 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:24:47: 3000000 INFO @ Tue, 02 Aug 2022 14:24:47: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:24:47: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:24:47: #1 total tags in treatment: 9037236 INFO @ Tue, 02 Aug 2022 14:24:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:24:47: #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 14:24:47: #1 tags after filtering in treatment: 9037236 INFO @ Tue, 02 Aug 2022 14:24:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:24:47: #1 finished! INFO @ Tue, 02 Aug 2022 14:24:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:24:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:24:48: #2 number of paired peaks: 786 WARNING @ Tue, 02 Aug 2022 14:24:48: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Tue, 02 Aug 2022 14:24:48: start model_add_line... INFO @ Tue, 02 Aug 2022 14:24:48: start X-correlation... INFO @ Tue, 02 Aug 2022 14:24:48: end of X-cor INFO @ Tue, 02 Aug 2022 14:24:48: #2 finished! INFO @ Tue, 02 Aug 2022 14:24:48: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 14:24:48: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 02 Aug 2022 14:24:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.10_model.r WARNING @ Tue, 02 Aug 2022 14:24:48: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:24:48: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 02 Aug 2022 14:24:48: #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 14:24:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:24:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:24:52: 4000000 INFO @ Tue, 02 Aug 2022 14:24:57: 5000000 INFO @ Tue, 02 Aug 2022 14:25:02: 6000000 INFO @ Tue, 02 Aug 2022 14:25:07: 7000000 INFO @ Tue, 02 Aug 2022 14:25:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:25:11: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:25:16: 9000000 INFO @ Tue, 02 Aug 2022 14:25:17: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:25:17: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:25:17: #1 total tags in treatment: 9037236 INFO @ Tue, 02 Aug 2022 14:25:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:25:17: #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 14:25:17: #1 tags after filtering in treatment: 9037236 INFO @ Tue, 02 Aug 2022 14:25:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:25:17: #1 finished! INFO @ Tue, 02 Aug 2022 14:25:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:25:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.10_summits.bed INFO @ Tue, 02 Aug 2022 14:25:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2107 records, 4 fields): 82 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:25:17: #2 number of paired peaks: 786 WARNING @ Tue, 02 Aug 2022 14:25:17: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Tue, 02 Aug 2022 14:25:17: start model_add_line... INFO @ Tue, 02 Aug 2022 14:25:17: start X-correlation... INFO @ Tue, 02 Aug 2022 14:25:18: end of X-cor INFO @ Tue, 02 Aug 2022 14:25:18: #2 finished! INFO @ Tue, 02 Aug 2022 14:25:18: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 14:25:18: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 02 Aug 2022 14:25:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.20_model.r WARNING @ Tue, 02 Aug 2022 14:25:18: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:25:18: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 02 Aug 2022 14:25:18: #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 14:25:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:25:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:25:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:25:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:25:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206522/SRX15206522.20_summits.bed INFO @ Tue, 02 Aug 2022 14:25:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (946 records, 4 fields): 27 millis CompletedMACS2peakCalling