Job ID = 14170561 SRX = SRX8689092 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6135217 spots for SRR12174284/SRR12174284.sra Written 6135217 spots for SRR12174284/SRR12174284.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170960 ("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: 00:02:33 6135217 reads; of these: 6135217 (100.00%) were unpaired; of these: 174621 (2.85%) aligned 0 times 3964915 (64.63%) aligned exactly 1 time 1995681 (32.53%) aligned >1 times 97.15% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 257402 / 5960596 = 0.0432 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 07:20:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.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 07:20:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:20:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:20:09: 1000000 INFO @ Sat, 11 Dec 2021 07:20:19: 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 07:20:28: 3000000 INFO @ Sat, 11 Dec 2021 07:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.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 07:20:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:20:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:20:37: 4000000 INFO @ Sat, 11 Dec 2021 07:20:39: 1000000 INFO @ Sat, 11 Dec 2021 07:20:47: 5000000 INFO @ Sat, 11 Dec 2021 07:20:48: 2000000 INFO @ Sat, 11 Dec 2021 07:20:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:20:53: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:20:53: #1 total tags in treatment: 5703194 INFO @ Sat, 11 Dec 2021 07:20:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:20:53: #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 07:20:53: #1 tags after filtering in treatment: 5703194 INFO @ Sat, 11 Dec 2021 07:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:20:53: #1 finished! INFO @ Sat, 11 Dec 2021 07:20:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:20:54: #2 number of paired peaks: 421 WARNING @ Sat, 11 Dec 2021 07:20:54: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Sat, 11 Dec 2021 07:20:54: start model_add_line... INFO @ Sat, 11 Dec 2021 07:20:54: start X-correlation... INFO @ Sat, 11 Dec 2021 07:20:54: end of X-cor INFO @ Sat, 11 Dec 2021 07:20:54: #2 finished! INFO @ Sat, 11 Dec 2021 07:20:54: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:20:54: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.05_model.r WARNING @ Sat, 11 Dec 2021 07:20:54: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:20:54: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:20:54: #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 07:20:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:20:54: #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 @ Sat, 11 Dec 2021 07:20:57: 3000000 INFO @ Sat, 11 Dec 2021 07:21:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.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 07:21:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:21:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:21:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:21:06: 4000000 INFO @ Sat, 11 Dec 2021 07:21:09: 1000000 INFO @ Sat, 11 Dec 2021 07:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.05_summits.bed INFO @ Sat, 11 Dec 2021 07:21:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1384 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:21:15: 5000000 INFO @ Sat, 11 Dec 2021 07:21:18: 2000000 INFO @ Sat, 11 Dec 2021 07:21:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:21:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:21:21: #1 total tags in treatment: 5703194 INFO @ Sat, 11 Dec 2021 07:21:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:21:21: #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 07:21:22: #1 tags after filtering in treatment: 5703194 INFO @ Sat, 11 Dec 2021 07:21:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:21:22: #1 finished! INFO @ Sat, 11 Dec 2021 07:21:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:21:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:21:22: #2 number of paired peaks: 421 WARNING @ Sat, 11 Dec 2021 07:21:22: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Sat, 11 Dec 2021 07:21:22: start model_add_line... INFO @ Sat, 11 Dec 2021 07:21:22: start X-correlation... INFO @ Sat, 11 Dec 2021 07:21:22: end of X-cor INFO @ Sat, 11 Dec 2021 07:21:22: #2 finished! INFO @ Sat, 11 Dec 2021 07:21:22: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:21:22: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:21:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.10_model.r WARNING @ Sat, 11 Dec 2021 07:21:22: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:21:22: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:21:22: #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 07:21:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:21:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:21:26: 3000000 INFO @ Sat, 11 Dec 2021 07:21:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:21:35: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:21:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:21:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:21:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.10_summits.bed INFO @ Sat, 11 Dec 2021 07:21:40: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1029 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:21:44: 5000000 INFO @ Sat, 11 Dec 2021 07:21:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:21:50: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:21:50: #1 total tags in treatment: 5703194 INFO @ Sat, 11 Dec 2021 07:21:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:21:50: #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 07:21:50: #1 tags after filtering in treatment: 5703194 INFO @ Sat, 11 Dec 2021 07:21:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:21:50: #1 finished! INFO @ Sat, 11 Dec 2021 07:21:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:21:51: #2 number of paired peaks: 421 WARNING @ Sat, 11 Dec 2021 07:21:51: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Sat, 11 Dec 2021 07:21:51: start model_add_line... INFO @ Sat, 11 Dec 2021 07:21:51: start X-correlation... INFO @ Sat, 11 Dec 2021 07:21:51: end of X-cor INFO @ Sat, 11 Dec 2021 07:21:51: #2 finished! INFO @ Sat, 11 Dec 2021 07:21:51: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:21:51: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.20_model.r WARNING @ Sat, 11 Dec 2021 07:21:51: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:21:51: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:21:51: #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 07:21:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:21:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:22:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:22:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:22:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:22:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689092/SRX8689092.20_summits.bed INFO @ Sat, 11 Dec 2021 07:22:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (653 records, 4 fields): 2 millis CompletedMACS2peakCalling