Job ID = 16436191 SRX = SRX15369014 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T02:02:56 prefetch.2.10.7: 1) Downloading 'SRR19308743'... 2022-08-02T02:02:56 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:03:34 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:03:34 prefetch.2.10.7: 1) 'SRR19308743' was downloaded successfully 2022-08-02T02:03:34 prefetch.2.10.7: 'SRR19308743' has 0 unresolved dependencies Read 20502489 spots for SRR19308743/SRR19308743.sra Written 20502489 spots for SRR19308743/SRR19308743.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436376 ("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: 00:15:07 20502489 reads; of these: 20502489 (100.00%) were unpaired; of these: 735979 (3.59%) aligned 0 times 11674129 (56.94%) aligned exactly 1 time 8092381 (39.47%) aligned >1 times 96.41% overall alignment rate Time searching: 00:15:07 Overall time: 00:15:07 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 12 files... [bam_rmdupse_core] 10398602 / 19766510 = 0.5261 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 11:26:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.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 11:26:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:26:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:26:17: 1000000 INFO @ Tue, 02 Aug 2022 11:26:25: 2000000 INFO @ Tue, 02 Aug 2022 11:26:32: 3000000 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 11:26:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.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 11:26:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:26:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:26:39: 4000000 INFO @ Tue, 02 Aug 2022 11:26:46: 1000000 INFO @ Tue, 02 Aug 2022 11:26:47: 5000000 INFO @ Tue, 02 Aug 2022 11:26:52: 2000000 INFO @ Tue, 02 Aug 2022 11:26:54: 6000000 INFO @ Tue, 02 Aug 2022 11:26:58: 3000000 INFO @ Tue, 02 Aug 2022 11:27:01: 7000000 INFO @ Tue, 02 Aug 2022 11:27:05: 4000000 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 11:27:09: 8000000 INFO @ Tue, 02 Aug 2022 11:27:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.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 11:27:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:27:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:27:12: 5000000 INFO @ Tue, 02 Aug 2022 11:27:16: 9000000 INFO @ Tue, 02 Aug 2022 11:27:17: 1000000 INFO @ Tue, 02 Aug 2022 11:27:19: 6000000 INFO @ Tue, 02 Aug 2022 11:27:19: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:27:19: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:27:19: #1 total tags in treatment: 9367908 INFO @ Tue, 02 Aug 2022 11:27:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:27:19: #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 11:27:20: #1 tags after filtering in treatment: 9367908 INFO @ Tue, 02 Aug 2022 11:27:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:27:20: #1 finished! INFO @ Tue, 02 Aug 2022 11:27:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:27:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:27:20: #2 number of paired peaks: 628 WARNING @ Tue, 02 Aug 2022 11:27:20: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Tue, 02 Aug 2022 11:27:20: start model_add_line... INFO @ Tue, 02 Aug 2022 11:27:20: start X-correlation... INFO @ Tue, 02 Aug 2022 11:27:21: end of X-cor INFO @ Tue, 02 Aug 2022 11:27:21: #2 finished! INFO @ Tue, 02 Aug 2022 11:27:21: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 11:27:21: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 11:27:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.05_model.r WARNING @ Tue, 02 Aug 2022 11:27:21: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:27:21: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 11:27:21: #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 11:27:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:27:25: 2000000 INFO @ Tue, 02 Aug 2022 11:27:27: 7000000 INFO @ Tue, 02 Aug 2022 11:27:32: 3000000 INFO @ Tue, 02 Aug 2022 11:27:34: 8000000 INFO @ Tue, 02 Aug 2022 11:27:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:27:40: 4000000 INFO @ Tue, 02 Aug 2022 11:27:41: 9000000 INFO @ Tue, 02 Aug 2022 11:27:44: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:27:44: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:27:44: #1 total tags in treatment: 9367908 INFO @ Tue, 02 Aug 2022 11:27:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:27:44: #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 11:27:44: #1 tags after filtering in treatment: 9367908 INFO @ Tue, 02 Aug 2022 11:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:27:44: #1 finished! INFO @ Tue, 02 Aug 2022 11:27:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:27:45: #2 number of paired peaks: 628 WARNING @ Tue, 02 Aug 2022 11:27:45: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Tue, 02 Aug 2022 11:27:45: start model_add_line... INFO @ Tue, 02 Aug 2022 11:27:45: start X-correlation... INFO @ Tue, 02 Aug 2022 11:27:45: end of X-cor INFO @ Tue, 02 Aug 2022 11:27:45: #2 finished! INFO @ Tue, 02 Aug 2022 11:27:45: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 11:27:45: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 11:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.10_model.r WARNING @ Tue, 02 Aug 2022 11:27:45: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:27:45: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 11:27:45: #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 11:27:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:27:47: 5000000 INFO @ Tue, 02 Aug 2022 11:27:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:27:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:27:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.05_summits.bed INFO @ Tue, 02 Aug 2022 11:27:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6640 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:27:55: 6000000 INFO @ Tue, 02 Aug 2022 11:28:02: 7000000 INFO @ Tue, 02 Aug 2022 11:28:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:28:09: 8000000 INFO @ Tue, 02 Aug 2022 11:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.10_summits.bed INFO @ Tue, 02 Aug 2022 11:28:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3277 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:28:17: 9000000 INFO @ Tue, 02 Aug 2022 11:28:20: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:28:20: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:28:20: #1 total tags in treatment: 9367908 INFO @ Tue, 02 Aug 2022 11:28:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:28:20: #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 11:28:20: #1 tags after filtering in treatment: 9367908 INFO @ Tue, 02 Aug 2022 11:28:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:28:20: #1 finished! INFO @ Tue, 02 Aug 2022 11:28:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:28:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:28:20: #2 number of paired peaks: 628 WARNING @ Tue, 02 Aug 2022 11:28:20: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Tue, 02 Aug 2022 11:28:20: start model_add_line... INFO @ Tue, 02 Aug 2022 11:28:21: start X-correlation... INFO @ Tue, 02 Aug 2022 11:28:21: end of X-cor INFO @ Tue, 02 Aug 2022 11:28:21: #2 finished! INFO @ Tue, 02 Aug 2022 11:28:21: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 11:28:21: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 11:28:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.20_model.r WARNING @ Tue, 02 Aug 2022 11:28:21: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:28:21: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 11:28:21: #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 11:28:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:28:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:28:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:28:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:28:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:28:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369014/SRX15369014.20_summits.bed INFO @ Tue, 02 Aug 2022 11:28:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1061 records, 4 fields): 35 millis CompletedMACS2peakCalling BigWig に変換しました。