Job ID = 14170464 SRX = SRX8689030 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5788568 spots for SRR12174384/SRR12174384.sra Written 5788568 spots for SRR12174384/SRR12174384.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170867 ("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: 00:02:55 5788568 reads; of these: 5788568 (100.00%) were unpaired; of these: 563266 (9.73%) aligned 0 times 3131036 (54.09%) aligned exactly 1 time 2094266 (36.18%) aligned >1 times 90.27% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 490492 / 5225302 = 0.0939 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 @ Sat, 11 Dec 2021 06:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.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 @ Sat, 11 Dec 2021 06:55:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:55:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:55:22: 1000000 INFO @ Sat, 11 Dec 2021 06:55:29: 2000000 INFO @ Sat, 11 Dec 2021 06:55:37: 3000000 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 @ Sat, 11 Dec 2021 06:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.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 @ Sat, 11 Dec 2021 06:55:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:55:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:55:45: 4000000 INFO @ Sat, 11 Dec 2021 06:55:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:55:50: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:55:50: #1 total tags in treatment: 4734810 INFO @ Sat, 11 Dec 2021 06:55:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:55:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:55:51: #1 tags after filtering in treatment: 4734810 INFO @ Sat, 11 Dec 2021 06:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:55:51: #1 finished! INFO @ Sat, 11 Dec 2021 06:55:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:55:51: #2 number of paired peaks: 631 WARNING @ Sat, 11 Dec 2021 06:55:51: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Sat, 11 Dec 2021 06:55:51: start model_add_line... INFO @ Sat, 11 Dec 2021 06:55:51: start X-correlation... INFO @ Sat, 11 Dec 2021 06:55:51: end of X-cor INFO @ Sat, 11 Dec 2021 06:55:51: #2 finished! INFO @ Sat, 11 Dec 2021 06:55:51: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 06:55:51: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 06:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.05_model.r WARNING @ Sat, 11 Dec 2021 06:55:51: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:55:51: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 06:55:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:55:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:55:53: 1000000 INFO @ Sat, 11 Dec 2021 06:56:02: 2000000 INFO @ Sat, 11 Dec 2021 06:56:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:56:10: 3000000 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 @ Sat, 11 Dec 2021 06:56:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:56:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:56:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.05_summits.bed INFO @ Sat, 11 Dec 2021 06:56:13: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1670 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:56:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.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 @ Sat, 11 Dec 2021 06:56:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:56:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:56:19: 4000000 INFO @ Sat, 11 Dec 2021 06:56:25: 1000000 INFO @ Sat, 11 Dec 2021 06:56:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:56:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:56:26: #1 total tags in treatment: 4734810 INFO @ Sat, 11 Dec 2021 06:56:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:56:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:56:26: #1 tags after filtering in treatment: 4734810 INFO @ Sat, 11 Dec 2021 06:56:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:56:26: #1 finished! INFO @ Sat, 11 Dec 2021 06:56:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:56:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:56:27: #2 number of paired peaks: 631 WARNING @ Sat, 11 Dec 2021 06:56:27: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Sat, 11 Dec 2021 06:56:27: start model_add_line... INFO @ Sat, 11 Dec 2021 06:56:27: start X-correlation... INFO @ Sat, 11 Dec 2021 06:56:27: end of X-cor INFO @ Sat, 11 Dec 2021 06:56:27: #2 finished! INFO @ Sat, 11 Dec 2021 06:56:27: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 06:56:27: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 06:56:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.10_model.r WARNING @ Sat, 11 Dec 2021 06:56:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:56:27: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 06:56:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:56:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:56:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:56:34: 2000000 INFO @ Sat, 11 Dec 2021 06:56:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:56:45: 3000000 INFO @ Sat, 11 Dec 2021 06:56:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:56:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:56:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.10_summits.bed INFO @ Sat, 11 Dec 2021 06:56:48: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1103 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:56:55: 4000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:57:02: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:57:02: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:57:02: #1 total tags in treatment: 4734810 INFO @ Sat, 11 Dec 2021 06:57:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:57:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:57:02: #1 tags after filtering in treatment: 4734810 INFO @ Sat, 11 Dec 2021 06:57:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:57:02: #1 finished! INFO @ Sat, 11 Dec 2021 06:57:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:57:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:57:03: #2 number of paired peaks: 631 WARNING @ Sat, 11 Dec 2021 06:57:03: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Sat, 11 Dec 2021 06:57:03: start model_add_line... INFO @ Sat, 11 Dec 2021 06:57:03: start X-correlation... INFO @ Sat, 11 Dec 2021 06:57:03: end of X-cor INFO @ Sat, 11 Dec 2021 06:57:03: #2 finished! INFO @ Sat, 11 Dec 2021 06:57:03: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 06:57:03: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 06:57:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.20_model.r WARNING @ Sat, 11 Dec 2021 06:57:03: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:57:03: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 06:57:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:57:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:57:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:57:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:57:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:57:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:57:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689030/SRX8689030.20_summits.bed INFO @ Sat, 11 Dec 2021 06:57:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (765 records, 4 fields): 2 millis CompletedMACS2peakCalling