Job ID = 14170518 SRX = SRX8689076 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7679244 spots for SRR12174309/SRR12174309.sra Written 7679244 spots for SRR12174309/SRR12174309.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170929 ("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: 00:03:06 7679244 reads; of these: 7679244 (100.00%) were unpaired; of these: 849007 (11.06%) aligned 0 times 4948051 (64.43%) aligned exactly 1 time 1882186 (24.51%) aligned >1 times 88.94% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 324415 / 6830237 = 0.0475 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 07:09:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.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 07:09:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:09:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:09:40: 1000000 INFO @ Sat, 11 Dec 2021 07:09:51: 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 07:09:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.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 07:09:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:09:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:10:02: 3000000 INFO @ Sat, 11 Dec 2021 07:10:07: 1000000 INFO @ Sat, 11 Dec 2021 07:10:13: 4000000 INFO @ Sat, 11 Dec 2021 07:10:15: 2000000 INFO @ Sat, 11 Dec 2021 07:10:23: 3000000 INFO @ Sat, 11 Dec 2021 07:10:25: 5000000 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 07:10:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.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 07:10:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:10:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:10:32: 4000000 INFO @ Sat, 11 Dec 2021 07:10:36: 6000000 INFO @ Sat, 11 Dec 2021 07:10:40: 5000000 INFO @ Sat, 11 Dec 2021 07:10:41: 1000000 INFO @ Sat, 11 Dec 2021 07:10:42: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:10:42: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:10:42: #1 total tags in treatment: 6505822 INFO @ Sat, 11 Dec 2021 07:10:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:10:42: #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 07:10:42: #1 tags after filtering in treatment: 6505822 INFO @ Sat, 11 Dec 2021 07:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:10:42: #1 finished! INFO @ Sat, 11 Dec 2021 07:10:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:10:42: #2 number of paired peaks: 277 WARNING @ Sat, 11 Dec 2021 07:10:42: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 11 Dec 2021 07:10:42: start model_add_line... INFO @ Sat, 11 Dec 2021 07:10:42: start X-correlation... INFO @ Sat, 11 Dec 2021 07:10:42: end of X-cor INFO @ Sat, 11 Dec 2021 07:10:42: #2 finished! INFO @ Sat, 11 Dec 2021 07:10:42: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:10:42: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:10:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.05_model.r WARNING @ Sat, 11 Dec 2021 07:10:42: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:10:42: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:10:42: #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 07:10:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:10:49: 6000000 INFO @ Sat, 11 Dec 2021 07:10:53: 2000000 INFO @ Sat, 11 Dec 2021 07:10:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:10:53: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:10:53: #1 total tags in treatment: 6505822 INFO @ Sat, 11 Dec 2021 07:10:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:10:53: #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 07:10:53: #1 tags after filtering in treatment: 6505822 INFO @ Sat, 11 Dec 2021 07:10:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:10:53: #1 finished! INFO @ Sat, 11 Dec 2021 07:10:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:10:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:10:54: #2 number of paired peaks: 277 WARNING @ Sat, 11 Dec 2021 07:10:54: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 11 Dec 2021 07:10:54: start model_add_line... INFO @ Sat, 11 Dec 2021 07:10:54: start X-correlation... INFO @ Sat, 11 Dec 2021 07:10:54: end of X-cor INFO @ Sat, 11 Dec 2021 07:10:54: #2 finished! INFO @ Sat, 11 Dec 2021 07:10:54: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:10:54: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:10:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.10_model.r WARNING @ Sat, 11 Dec 2021 07:10:54: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:10:54: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:10:54: #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 07:10:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:10:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:11:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:11:05: 3000000 INFO @ Sat, 11 Dec 2021 07:11:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.05_summits.bed INFO @ Sat, 11 Dec 2021 07:11:11: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1164 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:11:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:11:17: 4000000 INFO @ Sat, 11 Dec 2021 07:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.10_summits.bed INFO @ Sat, 11 Dec 2021 07:11:23: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (936 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:11:28: 5000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:11:40: 6000000 INFO @ Sat, 11 Dec 2021 07:11:45: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:11:45: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:11:45: #1 total tags in treatment: 6505822 INFO @ Sat, 11 Dec 2021 07:11:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:11:45: #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 07:11:45: #1 tags after filtering in treatment: 6505822 INFO @ Sat, 11 Dec 2021 07:11:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:11:45: #1 finished! INFO @ Sat, 11 Dec 2021 07:11:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:11:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:11:45: #2 number of paired peaks: 277 WARNING @ Sat, 11 Dec 2021 07:11:45: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 11 Dec 2021 07:11:45: start model_add_line... INFO @ Sat, 11 Dec 2021 07:11:45: start X-correlation... INFO @ Sat, 11 Dec 2021 07:11:45: end of X-cor INFO @ Sat, 11 Dec 2021 07:11:45: #2 finished! INFO @ Sat, 11 Dec 2021 07:11:45: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:11:45: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:11:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.20_model.r WARNING @ Sat, 11 Dec 2021 07:11:45: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:11:45: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:11:45: #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 07:11:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:11:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:12:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689076/SRX8689076.20_summits.bed INFO @ Sat, 11 Dec 2021 07:12:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 3 millis CompletedMACS2peakCalling