Job ID = 14166987 SRX = SRX7723720 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25320946 spots for SRR11084676/SRR11084676.sra Written 25320946 spots for SRR11084676/SRR11084676.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167333 ("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: 00:08:26 25320946 reads; of these: 25320946 (100.00%) were unpaired; of these: 13118019 (51.81%) aligned 0 times 8455778 (33.39%) aligned exactly 1 time 3747149 (14.80%) aligned >1 times 48.19% overall alignment rate Time searching: 00:08:26 Overall time: 00:08:26 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] 4613486 / 12202927 = 0.3781 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:40:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.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 @ Fri, 10 Dec 2021 08:40:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:40:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:40:49: 1000000 INFO @ Fri, 10 Dec 2021 08:40:56: 2000000 INFO @ Fri, 10 Dec 2021 08:41:02: 3000000 INFO @ Fri, 10 Dec 2021 08:41:09: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:41:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.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 @ Fri, 10 Dec 2021 08:41:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:41:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:41:16: 5000000 INFO @ Fri, 10 Dec 2021 08:41:22: 1000000 INFO @ Fri, 10 Dec 2021 08:41:25: 6000000 INFO @ Fri, 10 Dec 2021 08:41:30: 2000000 INFO @ Fri, 10 Dec 2021 08:41:34: 7000000 INFO @ Fri, 10 Dec 2021 08:41:39: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:41:39: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:41:39: #1 total tags in treatment: 7589441 INFO @ Fri, 10 Dec 2021 08:41:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:41:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:41:39: #1 tags after filtering in treatment: 7589441 INFO @ Fri, 10 Dec 2021 08:41:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:41:39: #1 finished! INFO @ Fri, 10 Dec 2021 08:41:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:41:39: 3000000 INFO @ Fri, 10 Dec 2021 08:41:40: #2 number of paired peaks: 149 WARNING @ Fri, 10 Dec 2021 08:41:40: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 10 Dec 2021 08:41:40: start model_add_line... INFO @ Fri, 10 Dec 2021 08:41:40: start X-correlation... INFO @ Fri, 10 Dec 2021 08:41:40: end of X-cor INFO @ Fri, 10 Dec 2021 08:41:40: #2 finished! INFO @ Fri, 10 Dec 2021 08:41:40: #2 predicted fragment length is 67 bps INFO @ Fri, 10 Dec 2021 08:41:40: #2 alternative fragment length(s) may be 67 bps INFO @ Fri, 10 Dec 2021 08:41:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05_model.r WARNING @ Fri, 10 Dec 2021 08:41:40: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:41:40: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Fri, 10 Dec 2021 08:41:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:41:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:41:40: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:41:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.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 @ Fri, 10 Dec 2021 08:41:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:41:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:41:48: 4000000 INFO @ Fri, 10 Dec 2021 08:41:52: 1000000 INFO @ Fri, 10 Dec 2021 08:41:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:41:57: 5000000 INFO @ Fri, 10 Dec 2021 08:42:00: 2000000 INFO @ Fri, 10 Dec 2021 08:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05_summits.bed INFO @ Fri, 10 Dec 2021 08:42:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1463 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:42:06: 6000000 INFO @ Fri, 10 Dec 2021 08:42:09: 3000000 INFO @ Fri, 10 Dec 2021 08:42:14: 7000000 INFO @ Fri, 10 Dec 2021 08:42:18: 4000000 INFO @ Fri, 10 Dec 2021 08:42:20: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:42:20: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:42:20: #1 total tags in treatment: 7589441 INFO @ Fri, 10 Dec 2021 08:42:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:42:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:42:20: #1 tags after filtering in treatment: 7589441 INFO @ Fri, 10 Dec 2021 08:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:42:20: #1 finished! INFO @ Fri, 10 Dec 2021 08:42:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:42:20: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:42:20: #2 number of paired peaks: 149 WARNING @ Fri, 10 Dec 2021 08:42:20: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 10 Dec 2021 08:42:20: start model_add_line... INFO @ Fri, 10 Dec 2021 08:42:20: start X-correlation... INFO @ Fri, 10 Dec 2021 08:42:20: end of X-cor INFO @ Fri, 10 Dec 2021 08:42:20: #2 finished! INFO @ Fri, 10 Dec 2021 08:42:20: #2 predicted fragment length is 67 bps INFO @ Fri, 10 Dec 2021 08:42:20: #2 alternative fragment length(s) may be 67 bps INFO @ Fri, 10 Dec 2021 08:42:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10_model.r WARNING @ Fri, 10 Dec 2021 08:42:20: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:42:20: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Fri, 10 Dec 2021 08:42:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:42:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:42:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:42:26: 5000000 INFO @ Fri, 10 Dec 2021 08:42:33: 6000000 INFO @ Fri, 10 Dec 2021 08:42:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:42:41: 7000000 INFO @ Fri, 10 Dec 2021 08:42:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:42:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:42:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10_summits.bed INFO @ Fri, 10 Dec 2021 08:42:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (953 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:42:45: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:42:45: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:42:45: #1 total tags in treatment: 7589441 INFO @ Fri, 10 Dec 2021 08:42:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:42:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:42:45: #1 tags after filtering in treatment: 7589441 INFO @ Fri, 10 Dec 2021 08:42:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:42:45: #1 finished! INFO @ Fri, 10 Dec 2021 08:42:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:42:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:42:46: #2 number of paired peaks: 149 WARNING @ Fri, 10 Dec 2021 08:42:46: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 10 Dec 2021 08:42:46: start model_add_line... INFO @ Fri, 10 Dec 2021 08:42:46: start X-correlation... INFO @ Fri, 10 Dec 2021 08:42:46: end of X-cor INFO @ Fri, 10 Dec 2021 08:42:46: #2 finished! INFO @ Fri, 10 Dec 2021 08:42:46: #2 predicted fragment length is 67 bps INFO @ Fri, 10 Dec 2021 08:42:46: #2 alternative fragment length(s) may be 67 bps INFO @ Fri, 10 Dec 2021 08:42:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20_model.r WARNING @ Fri, 10 Dec 2021 08:42:46: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:42:46: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Fri, 10 Dec 2021 08:42:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:42:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:42:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:43:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:43:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:43:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:43:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20_summits.bed INFO @ Fri, 10 Dec 2021 08:43:10: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 2 millis CompletedMACS2peakCalling