Job ID = 16438035 SRX = SRX12261344 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20491122 spots for SRR15972600/SRR15972600.sra Written 20491122 spots for SRR15972600/SRR15972600.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438106 ("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: 00:12:03 20491122 reads; of these: 20491122 (100.00%) were unpaired; of these: 881238 (4.30%) aligned 0 times 12259371 (59.83%) aligned exactly 1 time 7350513 (35.87%) aligned >1 times 95.70% overall alignment rate Time searching: 00:12:03 Overall time: 00:12:03 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_sort_core] merging from 8 files... [bam_rmdupse_core] 11444098 / 19609884 = 0.5836 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:37:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.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 @ Tue, 02 Aug 2022 13:37:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:37:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:37:44: 1000000 INFO @ Tue, 02 Aug 2022 13:37:50: 2000000 INFO @ Tue, 02 Aug 2022 13:37:55: 3000000 INFO @ Tue, 02 Aug 2022 13:38:01: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:38:07: 5000000 INFO @ Tue, 02 Aug 2022 13:38:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.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 @ Tue, 02 Aug 2022 13:38:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:38:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:38:13: 6000000 INFO @ Tue, 02 Aug 2022 13:38:15: 1000000 INFO @ Tue, 02 Aug 2022 13:38:19: 7000000 INFO @ Tue, 02 Aug 2022 13:38:21: 2000000 INFO @ Tue, 02 Aug 2022 13:38:25: 8000000 INFO @ Tue, 02 Aug 2022 13:38:26: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:38:26: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:38:26: #1 total tags in treatment: 8165786 INFO @ Tue, 02 Aug 2022 13:38:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:38:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:38:26: #1 tags after filtering in treatment: 8165786 INFO @ Tue, 02 Aug 2022 13:38:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:38:26: #1 finished! INFO @ Tue, 02 Aug 2022 13:38:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:38:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:38:27: #2 number of paired peaks: 948 WARNING @ Tue, 02 Aug 2022 13:38:27: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Tue, 02 Aug 2022 13:38:27: start model_add_line... INFO @ Tue, 02 Aug 2022 13:38:27: 3000000 INFO @ Tue, 02 Aug 2022 13:38:27: start X-correlation... INFO @ Tue, 02 Aug 2022 13:38:27: end of X-cor INFO @ Tue, 02 Aug 2022 13:38:27: #2 finished! INFO @ Tue, 02 Aug 2022 13:38:27: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 13:38:27: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 02 Aug 2022 13:38:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.05_model.r WARNING @ Tue, 02 Aug 2022 13:38:27: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:38:27: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 02 Aug 2022 13:38:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:38:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:38:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:38:33: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:38:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.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 @ Tue, 02 Aug 2022 13:38:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:38:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:38:39: 5000000 INFO @ Tue, 02 Aug 2022 13:38:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:38:44: 1000000 INFO @ Tue, 02 Aug 2022 13:38:45: 6000000 INFO @ Tue, 02 Aug 2022 13:38:51: 2000000 INFO @ Tue, 02 Aug 2022 13:38:51: 7000000 INFO @ Tue, 02 Aug 2022 13:38:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:38:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:38:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.05_summits.bed INFO @ Tue, 02 Aug 2022 13:38:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8279 records, 4 fields): 53 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:38:57: 3000000 INFO @ Tue, 02 Aug 2022 13:38:57: 8000000 INFO @ Tue, 02 Aug 2022 13:38:58: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:38:58: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:38:58: #1 total tags in treatment: 8165786 INFO @ Tue, 02 Aug 2022 13:38:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:38:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:38:58: #1 tags after filtering in treatment: 8165786 INFO @ Tue, 02 Aug 2022 13:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:38:58: #1 finished! INFO @ Tue, 02 Aug 2022 13:38:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:38:59: #2 number of paired peaks: 948 WARNING @ Tue, 02 Aug 2022 13:38:59: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Tue, 02 Aug 2022 13:38:59: start model_add_line... INFO @ Tue, 02 Aug 2022 13:38:59: start X-correlation... INFO @ Tue, 02 Aug 2022 13:38:59: end of X-cor INFO @ Tue, 02 Aug 2022 13:38:59: #2 finished! INFO @ Tue, 02 Aug 2022 13:38:59: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 13:38:59: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 02 Aug 2022 13:38:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.10_model.r WARNING @ Tue, 02 Aug 2022 13:38:59: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:38:59: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 02 Aug 2022 13:38:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:38:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:38:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:39:03: 4000000 INFO @ Tue, 02 Aug 2022 13:39:09: 5000000 INFO @ Tue, 02 Aug 2022 13:39:14: 6000000 INFO @ Tue, 02 Aug 2022 13:39:16: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:39:20: 7000000 INFO @ Tue, 02 Aug 2022 13:39:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:39:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:39:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.10_summits.bed INFO @ Tue, 02 Aug 2022 13:39:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3570 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:39:26: 8000000 INFO @ Tue, 02 Aug 2022 13:39:27: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:39:27: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:39:27: #1 total tags in treatment: 8165786 INFO @ Tue, 02 Aug 2022 13:39:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:39:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:39:27: #1 tags after filtering in treatment: 8165786 INFO @ Tue, 02 Aug 2022 13:39:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:39:27: #1 finished! INFO @ Tue, 02 Aug 2022 13:39:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:39:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:39:28: #2 number of paired peaks: 948 WARNING @ Tue, 02 Aug 2022 13:39:28: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Tue, 02 Aug 2022 13:39:28: start model_add_line... INFO @ Tue, 02 Aug 2022 13:39:28: start X-correlation... INFO @ Tue, 02 Aug 2022 13:39:28: end of X-cor INFO @ Tue, 02 Aug 2022 13:39:28: #2 finished! INFO @ Tue, 02 Aug 2022 13:39:28: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 13:39:28: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 02 Aug 2022 13:39:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.20_model.r WARNING @ Tue, 02 Aug 2022 13:39:28: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:39:28: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 02 Aug 2022 13:39:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:39:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:39:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:39:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261344/SRX12261344.20_summits.bed INFO @ Tue, 02 Aug 2022 13:39:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1031 records, 4 fields): 34 millis CompletedMACS2peakCalling