Job ID = 14170921 SRX = SRX8689071 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:00 7462548 reads; of these: 7462548 (100.00%) were unpaired; of these: 381259 (5.11%) aligned 0 times 4964166 (66.52%) aligned exactly 1 time 2117123 (28.37%) aligned >1 times 94.89% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 1627301 / 7081289 = 0.2298 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 09:04:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.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 09:04:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:04:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:04:27: 1000000 INFO @ Sat, 11 Dec 2021 09:04:34: 2000000 INFO @ Sat, 11 Dec 2021 09:04:41: 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 09:04:48: 4000000 INFO @ Sat, 11 Dec 2021 09:04:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.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 09:04:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:04:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:04:56: 1000000 INFO @ Sat, 11 Dec 2021 09:04:56: 5000000 INFO @ Sat, 11 Dec 2021 09:05:00: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:05:00: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:05:00: #1 total tags in treatment: 5453988 INFO @ Sat, 11 Dec 2021 09:05:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:05:00: #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 09:05:00: #1 tags after filtering in treatment: 5453984 INFO @ Sat, 11 Dec 2021 09:05:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:05:00: #1 finished! INFO @ Sat, 11 Dec 2021 09:05:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:05:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:05:01: #2 number of paired peaks: 387 WARNING @ Sat, 11 Dec 2021 09:05:01: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Sat, 11 Dec 2021 09:05:01: start model_add_line... INFO @ Sat, 11 Dec 2021 09:05:01: start X-correlation... INFO @ Sat, 11 Dec 2021 09:05:01: end of X-cor INFO @ Sat, 11 Dec 2021 09:05:01: #2 finished! INFO @ Sat, 11 Dec 2021 09:05:01: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 09:05:01: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 09:05:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.05_model.r WARNING @ Sat, 11 Dec 2021 09:05:01: #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 09:05:01: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 09:05:01: #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 09:05:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:05:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:05:02: 2000000 INFO @ Sat, 11 Dec 2021 09:05:08: 3000000 INFO @ Sat, 11 Dec 2021 09:05:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:05:14: 4000000 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 09:05:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:05:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:05:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.05_summits.bed INFO @ Sat, 11 Dec 2021 09:05:18: Done! pass1 - making usageList (437 chroms): 1 millis pass2 - checking and writing primary data (1205 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.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 09:05:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:05:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:05:21: 5000000 INFO @ Sat, 11 Dec 2021 09:05:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:05:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:05:24: #1 total tags in treatment: 5453988 INFO @ Sat, 11 Dec 2021 09:05:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:05:24: #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 09:05:24: #1 tags after filtering in treatment: 5453984 INFO @ Sat, 11 Dec 2021 09:05:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:05:24: #1 finished! INFO @ Sat, 11 Dec 2021 09:05:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:05:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:05:25: #2 number of paired peaks: 387 WARNING @ Sat, 11 Dec 2021 09:05:25: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Sat, 11 Dec 2021 09:05:25: start model_add_line... INFO @ Sat, 11 Dec 2021 09:05:25: start X-correlation... INFO @ Sat, 11 Dec 2021 09:05:25: end of X-cor INFO @ Sat, 11 Dec 2021 09:05:25: #2 finished! INFO @ Sat, 11 Dec 2021 09:05:25: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 09:05:25: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 09:05:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.10_model.r WARNING @ Sat, 11 Dec 2021 09:05:25: #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 09:05:25: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 09:05:25: #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 09:05:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:05:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:05:26: 1000000 INFO @ Sat, 11 Dec 2021 09:05:33: 2000000 INFO @ Sat, 11 Dec 2021 09:05:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:05:40: 3000000 INFO @ Sat, 11 Dec 2021 09:05:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:05:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:05:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.10_summits.bed INFO @ Sat, 11 Dec 2021 09:05:41: Done! pass1 - making usageList (218 chroms): 1 millis pass2 - checking and writing primary data (486 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:05:47: 4000000 INFO @ Sat, 11 Dec 2021 09:05:54: 5000000 INFO @ Sat, 11 Dec 2021 09:05:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:05:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:05:57: #1 total tags in treatment: 5453988 INFO @ Sat, 11 Dec 2021 09:05:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:05:57: #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 09:05:57: #1 tags after filtering in treatment: 5453984 INFO @ Sat, 11 Dec 2021 09:05:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:05:57: #1 finished! INFO @ Sat, 11 Dec 2021 09:05:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:05:57: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:05:58: #2 number of paired peaks: 387 WARNING @ Sat, 11 Dec 2021 09:05:58: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Sat, 11 Dec 2021 09:05:58: start model_add_line... INFO @ Sat, 11 Dec 2021 09:05:58: start X-correlation... INFO @ Sat, 11 Dec 2021 09:05:58: end of X-cor INFO @ Sat, 11 Dec 2021 09:05:58: #2 finished! INFO @ Sat, 11 Dec 2021 09:05:58: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 09:05:58: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 09:05:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.20_model.r WARNING @ Sat, 11 Dec 2021 09:05:58: #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 09:05:58: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 09:05:58: #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 09:05:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:05:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:06:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:06:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:06:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:06:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689071/SRX8689071.20_summits.bed INFO @ Sat, 11 Dec 2021 09:06:15: Done! pass1 - making usageList (118 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 5 millis CompletedMACS2peakCalling