Job ID = 14170417 SRX = SRX8784751 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5817596 spots for SRR12280881/SRR12280881.sra Written 5817596 spots for SRR12280881/SRR12280881.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170813 ("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: 00:02:28 5817596 reads; of these: 5817596 (100.00%) were unpaired; of these: 360447 (6.20%) aligned 0 times 4706974 (80.91%) aligned exactly 1 time 750175 (12.89%) aligned >1 times 93.80% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 298837 / 5457149 = 0.0548 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 06:49:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.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 06:49:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:49:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:49:27: 1000000 INFO @ Sat, 11 Dec 2021 06:49:34: 2000000 INFO @ Sat, 11 Dec 2021 06:49:40: 3000000 INFO @ Sat, 11 Dec 2021 06:49:46: 4000000 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 06:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.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 06:49:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:49:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:49:53: 5000000 INFO @ Sat, 11 Dec 2021 06:49:54: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:49:54: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:49:54: #1 total tags in treatment: 5158312 INFO @ Sat, 11 Dec 2021 06:49:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:49:54: #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 06:49:54: #1 tags after filtering in treatment: 5158312 INFO @ Sat, 11 Dec 2021 06:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:49:54: #1 finished! INFO @ Sat, 11 Dec 2021 06:49:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:49:54: #2 number of paired peaks: 207 WARNING @ Sat, 11 Dec 2021 06:49:54: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sat, 11 Dec 2021 06:49:54: start model_add_line... INFO @ Sat, 11 Dec 2021 06:49:54: start X-correlation... INFO @ Sat, 11 Dec 2021 06:49:54: end of X-cor INFO @ Sat, 11 Dec 2021 06:49:54: #2 finished! INFO @ Sat, 11 Dec 2021 06:49:54: #2 predicted fragment length is 129 bps INFO @ Sat, 11 Dec 2021 06:49:54: #2 alternative fragment length(s) may be 129,147,594 bps INFO @ Sat, 11 Dec 2021 06:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.05_model.r WARNING @ Sat, 11 Dec 2021 06:49:54: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:49:54: #2 You may need to consider one of the other alternative d(s): 129,147,594 WARNING @ Sat, 11 Dec 2021 06:49:54: #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 06:49:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:49:59: 1000000 INFO @ Sat, 11 Dec 2021 06:50:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:50:07: 2000000 INFO @ Sat, 11 Dec 2021 06:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.05_summits.bed INFO @ Sat, 11 Dec 2021 06:50:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (684 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:50:14: 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 06:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.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 06:50:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:50:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:50:22: 4000000 INFO @ Sat, 11 Dec 2021 06:50:28: 1000000 INFO @ Sat, 11 Dec 2021 06:50:30: 5000000 INFO @ Sat, 11 Dec 2021 06:50:32: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:50:32: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:50:32: #1 total tags in treatment: 5158312 INFO @ Sat, 11 Dec 2021 06:50:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:50:32: #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 06:50:32: #1 tags after filtering in treatment: 5158312 INFO @ Sat, 11 Dec 2021 06:50:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:50:32: #1 finished! INFO @ Sat, 11 Dec 2021 06:50:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:50:32: #2 number of paired peaks: 207 WARNING @ Sat, 11 Dec 2021 06:50:32: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sat, 11 Dec 2021 06:50:32: start model_add_line... INFO @ Sat, 11 Dec 2021 06:50:32: start X-correlation... INFO @ Sat, 11 Dec 2021 06:50:32: end of X-cor INFO @ Sat, 11 Dec 2021 06:50:32: #2 finished! INFO @ Sat, 11 Dec 2021 06:50:32: #2 predicted fragment length is 129 bps INFO @ Sat, 11 Dec 2021 06:50:32: #2 alternative fragment length(s) may be 129,147,594 bps INFO @ Sat, 11 Dec 2021 06:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.10_model.r WARNING @ Sat, 11 Dec 2021 06:50:32: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:50:32: #2 You may need to consider one of the other alternative d(s): 129,147,594 WARNING @ Sat, 11 Dec 2021 06:50:32: #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 06:50:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:50:35: 2000000 INFO @ Sat, 11 Dec 2021 06:50:42: 3000000 INFO @ Sat, 11 Dec 2021 06:50:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:50:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:50:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:50:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.10_summits.bed INFO @ Sat, 11 Dec 2021 06:50:48: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:50:49: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:50:56: 5000000 INFO @ Sat, 11 Dec 2021 06:50:57: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:50:57: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:50:57: #1 total tags in treatment: 5158312 INFO @ Sat, 11 Dec 2021 06:50:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:50:57: #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 06:50:57: #1 tags after filtering in treatment: 5158312 INFO @ Sat, 11 Dec 2021 06:50:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:50:57: #1 finished! INFO @ Sat, 11 Dec 2021 06:50:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:50:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:50:58: #2 number of paired peaks: 207 WARNING @ Sat, 11 Dec 2021 06:50:58: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sat, 11 Dec 2021 06:50:58: start model_add_line... INFO @ Sat, 11 Dec 2021 06:50:58: start X-correlation... INFO @ Sat, 11 Dec 2021 06:50:58: end of X-cor INFO @ Sat, 11 Dec 2021 06:50:58: #2 finished! INFO @ Sat, 11 Dec 2021 06:50:58: #2 predicted fragment length is 129 bps INFO @ Sat, 11 Dec 2021 06:50:58: #2 alternative fragment length(s) may be 129,147,594 bps INFO @ Sat, 11 Dec 2021 06:50:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.20_model.r WARNING @ Sat, 11 Dec 2021 06:50:58: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:50:58: #2 You may need to consider one of the other alternative d(s): 129,147,594 WARNING @ Sat, 11 Dec 2021 06:50:58: #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 06:50:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:50:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:51:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784751/SRX8784751.20_summits.bed INFO @ Sat, 11 Dec 2021 06:51:15: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (83 records, 4 fields): 1 millis CompletedMACS2peakCalling