Job ID = 14167252 SRX = SRX8688917 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6590961 spots for SRR12174318/SRR12174318.sra Written 6590961 spots for SRR12174318/SRR12174318.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167853 ("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: 00:02:37 6590961 reads; of these: 6590961 (100.00%) were unpaired; of these: 220568 (3.35%) aligned 0 times 4642631 (70.44%) aligned exactly 1 time 1727762 (26.21%) aligned >1 times 96.65% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 267104 / 6370393 = 0.0419 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 @ Fri, 10 Dec 2021 11:24:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.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 @ Fri, 10 Dec 2021 11:24:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:24:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:25:07: 1000000 INFO @ Fri, 10 Dec 2021 11:25:17: 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 @ Fri, 10 Dec 2021 11:25:26: 3000000 INFO @ Fri, 10 Dec 2021 11:25:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.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 @ Fri, 10 Dec 2021 11:25:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:25:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:25:35: 4000000 INFO @ Fri, 10 Dec 2021 11:25:37: 1000000 INFO @ Fri, 10 Dec 2021 11:25:45: 5000000 INFO @ Fri, 10 Dec 2021 11:25:47: 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 @ Fri, 10 Dec 2021 11:25:55: 6000000 INFO @ Fri, 10 Dec 2021 11:25:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:25:56: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:25:56: #1 total tags in treatment: 6103289 INFO @ Fri, 10 Dec 2021 11:25:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:25:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:25:56: #1 tags after filtering in treatment: 6103289 INFO @ Fri, 10 Dec 2021 11:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:25:56: #1 finished! INFO @ Fri, 10 Dec 2021 11:25:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:25:57: #2 number of paired peaks: 376 WARNING @ Fri, 10 Dec 2021 11:25:57: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Fri, 10 Dec 2021 11:25:57: start model_add_line... INFO @ Fri, 10 Dec 2021 11:25:57: start X-correlation... INFO @ Fri, 10 Dec 2021 11:25:57: end of X-cor INFO @ Fri, 10 Dec 2021 11:25:57: #2 finished! INFO @ Fri, 10 Dec 2021 11:25:57: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 11:25:57: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 11:25:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.05_model.r WARNING @ Fri, 10 Dec 2021 11:25:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:25:57: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 11:25:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:25:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:25:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:25:57: 3000000 INFO @ Fri, 10 Dec 2021 11:25:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.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 @ Fri, 10 Dec 2021 11:25:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:25:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:26:06: 4000000 INFO @ Fri, 10 Dec 2021 11:26:07: 1000000 INFO @ Fri, 10 Dec 2021 11:26:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.05_summits.bed INFO @ Fri, 10 Dec 2021 11:26:16: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1393 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:26:17: 5000000 INFO @ Fri, 10 Dec 2021 11:26:17: 2000000 INFO @ Fri, 10 Dec 2021 11:26:26: 6000000 INFO @ Fri, 10 Dec 2021 11:26:27: 3000000 INFO @ Fri, 10 Dec 2021 11:26:27: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:26:27: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:26:27: #1 total tags in treatment: 6103289 INFO @ Fri, 10 Dec 2021 11:26:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:26:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:26:27: #1 tags after filtering in treatment: 6103289 INFO @ Fri, 10 Dec 2021 11:26:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:26:27: #1 finished! INFO @ Fri, 10 Dec 2021 11:26:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:26:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:26:27: #2 number of paired peaks: 376 WARNING @ Fri, 10 Dec 2021 11:26:27: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Fri, 10 Dec 2021 11:26:27: start model_add_line... INFO @ Fri, 10 Dec 2021 11:26:27: start X-correlation... INFO @ Fri, 10 Dec 2021 11:26:27: end of X-cor INFO @ Fri, 10 Dec 2021 11:26:27: #2 finished! INFO @ Fri, 10 Dec 2021 11:26:27: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 11:26:28: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 11:26:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.10_model.r WARNING @ Fri, 10 Dec 2021 11:26:28: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:26:28: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 11:26:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:26:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:26:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:26:36: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:26:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:26:45: 5000000 INFO @ Fri, 10 Dec 2021 11:26:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:26:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:26:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.10_summits.bed INFO @ Fri, 10 Dec 2021 11:26:47: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1133 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:26:56: 6000000 INFO @ Fri, 10 Dec 2021 11:26:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:26:57: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:26:57: #1 total tags in treatment: 6103289 INFO @ Fri, 10 Dec 2021 11:26:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:26:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:26:57: #1 tags after filtering in treatment: 6103289 INFO @ Fri, 10 Dec 2021 11:26:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:26:57: #1 finished! INFO @ Fri, 10 Dec 2021 11:26:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:26:57: #2 number of paired peaks: 376 WARNING @ Fri, 10 Dec 2021 11:26:57: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Fri, 10 Dec 2021 11:26:57: start model_add_line... INFO @ Fri, 10 Dec 2021 11:26:57: start X-correlation... INFO @ Fri, 10 Dec 2021 11:26:57: end of X-cor INFO @ Fri, 10 Dec 2021 11:26:57: #2 finished! INFO @ Fri, 10 Dec 2021 11:26:57: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 11:26:57: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 11:26:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.20_model.r WARNING @ Fri, 10 Dec 2021 11:26:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:26:57: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 11:26:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:26:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:26:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:27:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:27:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:27:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688917/SRX8688917.20_summits.bed INFO @ Fri, 10 Dec 2021 11:27:16: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (772 records, 4 fields): 3 millis CompletedMACS2peakCalling