Job ID = 14170491 SRX = SRX8689052 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6005350 spots for SRR12174195/SRR12174195.sra Written 6005350 spots for SRR12174195/SRR12174195.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170893 ("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: 00:01:52 6005350 reads; of these: 6005350 (100.00%) were unpaired; of these: 1130279 (18.82%) aligned 0 times 4017709 (66.90%) aligned exactly 1 time 857362 (14.28%) aligned >1 times 81.18% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 146633 / 4875071 = 0.0301 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 07:00:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.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 07:00:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:00:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:00:52: 1000000 INFO @ Sat, 11 Dec 2021 07:01:01: 2000000 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 07:01:11: 3000000 INFO @ Sat, 11 Dec 2021 07:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.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 07:01:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:01:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:20: 4000000 INFO @ Sat, 11 Dec 2021 07:01:26: 1000000 INFO @ Sat, 11 Dec 2021 07:01:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:01:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:01:27: #1 total tags in treatment: 4728438 INFO @ Sat, 11 Dec 2021 07:01:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:01:27: #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 07:01:27: #1 tags after filtering in treatment: 4728438 INFO @ Sat, 11 Dec 2021 07:01:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:01:27: #1 finished! INFO @ Sat, 11 Dec 2021 07:01:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:01:28: #2 number of paired peaks: 216 WARNING @ Sat, 11 Dec 2021 07:01:28: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sat, 11 Dec 2021 07:01:28: start model_add_line... INFO @ Sat, 11 Dec 2021 07:01:28: start X-correlation... INFO @ Sat, 11 Dec 2021 07:01:28: end of X-cor INFO @ Sat, 11 Dec 2021 07:01:28: #2 finished! INFO @ Sat, 11 Dec 2021 07:01:28: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 07:01:28: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 07:01:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.05_model.r WARNING @ Sat, 11 Dec 2021 07:01:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:01:28: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 07:01:28: #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 07:01:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:01:38: 2000000 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 07:01:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.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 07:01:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:01:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.05_summits.bed INFO @ Sat, 11 Dec 2021 07:01:49: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1082 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:01:51: 3000000 INFO @ Sat, 11 Dec 2021 07:01:51: 1000000 INFO @ Sat, 11 Dec 2021 07:02:00: 2000000 INFO @ Sat, 11 Dec 2021 07:02:04: 4000000 INFO @ Sat, 11 Dec 2021 07:02:08: 3000000 INFO @ Sat, 11 Dec 2021 07:02:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:02:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:02:13: #1 total tags in treatment: 4728438 INFO @ Sat, 11 Dec 2021 07:02:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:02:13: #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 07:02:13: #1 tags after filtering in treatment: 4728438 INFO @ Sat, 11 Dec 2021 07:02:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:02:13: #1 finished! INFO @ Sat, 11 Dec 2021 07:02:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:02:13: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:02:14: #2 number of paired peaks: 216 WARNING @ Sat, 11 Dec 2021 07:02:14: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sat, 11 Dec 2021 07:02:14: start model_add_line... INFO @ Sat, 11 Dec 2021 07:02:14: start X-correlation... INFO @ Sat, 11 Dec 2021 07:02:14: end of X-cor INFO @ Sat, 11 Dec 2021 07:02:14: #2 finished! INFO @ Sat, 11 Dec 2021 07:02:14: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 07:02:14: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 07:02:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.10_model.r WARNING @ Sat, 11 Dec 2021 07:02:14: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:02:14: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 07:02:14: #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 07:02:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:02:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:02:17: 4000000 INFO @ Sat, 11 Dec 2021 07:02:23: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:02:23: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:02:23: #1 total tags in treatment: 4728438 INFO @ Sat, 11 Dec 2021 07:02:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:02:23: #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 07:02:23: #1 tags after filtering in treatment: 4728438 INFO @ Sat, 11 Dec 2021 07:02:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:02:23: #1 finished! INFO @ Sat, 11 Dec 2021 07:02:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:02:23: #2 number of paired peaks: 216 WARNING @ Sat, 11 Dec 2021 07:02:23: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sat, 11 Dec 2021 07:02:23: start model_add_line... INFO @ Sat, 11 Dec 2021 07:02:23: start X-correlation... INFO @ Sat, 11 Dec 2021 07:02:23: end of X-cor INFO @ Sat, 11 Dec 2021 07:02:23: #2 finished! INFO @ Sat, 11 Dec 2021 07:02:23: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 07:02:23: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 07:02:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.20_model.r WARNING @ Sat, 11 Dec 2021 07:02:23: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:02:23: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 07:02:23: #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 07:02:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:02:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:02:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:02:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.10_summits.bed INFO @ Sat, 11 Dec 2021 07:02:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (811 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:02:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689052/SRX8689052.20_summits.bed INFO @ Sat, 11 Dec 2021 07:02:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 2 millis CompletedMACS2peakCalling