Job ID = 14167247 SRX = SRX8688912 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7218512 spots for SRR12174313/SRR12174313.sra Written 7218512 spots for SRR12174313/SRR12174313.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167826 ("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 7218512 reads; of these: 7218512 (100.00%) were unpaired; of these: 318103 (4.41%) aligned 0 times 4578419 (63.43%) aligned exactly 1 time 2321990 (32.17%) aligned >1 times 95.59% 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] 473283 / 6900409 = 0.0686 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 11:22:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.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 11:22:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:22:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:22:55: 1000000 INFO @ Fri, 10 Dec 2021 11:23:01: 2000000 INFO @ Fri, 10 Dec 2021 11:23:08: 3000000 INFO @ Fri, 10 Dec 2021 11:23:14: 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 @ Fri, 10 Dec 2021 11:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.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 11:23:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:23:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:23:21: 5000000 INFO @ Fri, 10 Dec 2021 11:23:25: 1000000 INFO @ Fri, 10 Dec 2021 11:23:28: 6000000 INFO @ Fri, 10 Dec 2021 11:23:31: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:23:31: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:23:31: #1 total tags in treatment: 6427126 INFO @ Fri, 10 Dec 2021 11:23:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:23:31: #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 11:23:31: #1 tags after filtering in treatment: 6427126 INFO @ Fri, 10 Dec 2021 11:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:23:31: #1 finished! INFO @ Fri, 10 Dec 2021 11:23:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:23:31: #2 number of paired peaks: 475 WARNING @ Fri, 10 Dec 2021 11:23:31: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Fri, 10 Dec 2021 11:23:31: start model_add_line... INFO @ Fri, 10 Dec 2021 11:23:31: start X-correlation... INFO @ Fri, 10 Dec 2021 11:23:31: end of X-cor INFO @ Fri, 10 Dec 2021 11:23:31: #2 finished! INFO @ Fri, 10 Dec 2021 11:23:31: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 11:23:31: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 11:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.05_model.r WARNING @ Fri, 10 Dec 2021 11:23:31: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:23:31: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 11:23:31: #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 11:23:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:23:31: 2000000 INFO @ Fri, 10 Dec 2021 11:23:37: 3000000 INFO @ Fri, 10 Dec 2021 11:23:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:23:44: 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 @ Fri, 10 Dec 2021 11:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.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 11:23:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:23:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:23:50: 5000000 INFO @ Fri, 10 Dec 2021 11:23:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:23:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.05_summits.bed INFO @ Fri, 10 Dec 2021 11:23:50: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1567 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:23:55: 1000000 INFO @ Fri, 10 Dec 2021 11:23:56: 6000000 INFO @ Fri, 10 Dec 2021 11:23:58: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:23:58: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:23:58: #1 total tags in treatment: 6427126 INFO @ Fri, 10 Dec 2021 11:23:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:23:58: #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 11:23:58: #1 tags after filtering in treatment: 6427126 INFO @ Fri, 10 Dec 2021 11:23:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:23:58: #1 finished! INFO @ Fri, 10 Dec 2021 11:23:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:23:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:23:59: #2 number of paired peaks: 475 WARNING @ Fri, 10 Dec 2021 11:23:59: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Fri, 10 Dec 2021 11:23:59: start model_add_line... INFO @ Fri, 10 Dec 2021 11:23:59: start X-correlation... INFO @ Fri, 10 Dec 2021 11:23:59: end of X-cor INFO @ Fri, 10 Dec 2021 11:23:59: #2 finished! INFO @ Fri, 10 Dec 2021 11:23:59: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 11:23:59: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 11:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.10_model.r WARNING @ Fri, 10 Dec 2021 11:23:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:23:59: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 11:23:59: #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 11:23:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:23:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:24:01: 2000000 INFO @ Fri, 10 Dec 2021 11:24:07: 3000000 INFO @ Fri, 10 Dec 2021 11:24:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:24:13: 4000000 INFO @ Fri, 10 Dec 2021 11:24:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:24:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:24:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.10_summits.bed INFO @ Fri, 10 Dec 2021 11:24:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1334 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:24:19: 5000000 INFO @ Fri, 10 Dec 2021 11:24:25: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:24:28: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:24:28: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:24:28: #1 total tags in treatment: 6427126 INFO @ Fri, 10 Dec 2021 11:24:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:24:28: #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 11:24:28: #1 tags after filtering in treatment: 6427126 INFO @ Fri, 10 Dec 2021 11:24:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:24:28: #1 finished! INFO @ Fri, 10 Dec 2021 11:24:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:24:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:24:28: #2 number of paired peaks: 475 WARNING @ Fri, 10 Dec 2021 11:24:28: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Fri, 10 Dec 2021 11:24:28: start model_add_line... INFO @ Fri, 10 Dec 2021 11:24:28: start X-correlation... INFO @ Fri, 10 Dec 2021 11:24:28: end of X-cor INFO @ Fri, 10 Dec 2021 11:24:28: #2 finished! INFO @ Fri, 10 Dec 2021 11:24:28: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 11:24:28: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 11:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.20_model.r WARNING @ Fri, 10 Dec 2021 11:24:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:24:29: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 11:24:29: #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 11:24:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:24:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:24:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:24:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:24:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688912/SRX8688912.20_summits.bed INFO @ Fri, 10 Dec 2021 11:24:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1005 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。