Job ID = 14171313 SRX = SRX9986144 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24995034 spots for SRR13591507/SRR13591507.sra Written 24995034 spots for SRR13591507/SRR13591507.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171795 ("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: 00:11:23 24995034 reads; of these: 24995034 (100.00%) were unpaired; of these: 1041948 (4.17%) aligned 0 times 12836070 (51.35%) aligned exactly 1 time 11117016 (44.48%) aligned >1 times 95.83% overall alignment rate Time searching: 00:11:23 Overall time: 00:11:23 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 12 files... [bam_rmdupse_core] 6952418 / 23953086 = 0.2903 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 11:29:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.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 11:29:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:29:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:29:22: 1000000 INFO @ Sat, 11 Dec 2021 11:29:28: 2000000 INFO @ Sat, 11 Dec 2021 11:29:34: 3000000 INFO @ Sat, 11 Dec 2021 11:29:40: 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 11:29:45: 5000000 INFO @ Sat, 11 Dec 2021 11:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.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 11:29:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:29:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:29:51: 6000000 INFO @ Sat, 11 Dec 2021 11:29:52: 1000000 INFO @ Sat, 11 Dec 2021 11:29:57: 2000000 INFO @ Sat, 11 Dec 2021 11:29:57: 7000000 INFO @ Sat, 11 Dec 2021 11:30:03: 3000000 INFO @ Sat, 11 Dec 2021 11:30:03: 8000000 INFO @ Sat, 11 Dec 2021 11:30:08: 4000000 INFO @ Sat, 11 Dec 2021 11:30:09: 9000000 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 11:30:14: 5000000 INFO @ Sat, 11 Dec 2021 11:30:15: 10000000 INFO @ Sat, 11 Dec 2021 11:30:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.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 11:30:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:30:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:30:20: 6000000 INFO @ Sat, 11 Dec 2021 11:30:21: 11000000 INFO @ Sat, 11 Dec 2021 11:30:23: 1000000 INFO @ Sat, 11 Dec 2021 11:30:26: 7000000 INFO @ Sat, 11 Dec 2021 11:30:27: 12000000 INFO @ Sat, 11 Dec 2021 11:30:29: 2000000 INFO @ Sat, 11 Dec 2021 11:30:32: 8000000 INFO @ Sat, 11 Dec 2021 11:30:33: 13000000 INFO @ Sat, 11 Dec 2021 11:30:35: 3000000 INFO @ Sat, 11 Dec 2021 11:30:38: 9000000 INFO @ Sat, 11 Dec 2021 11:30:39: 14000000 INFO @ Sat, 11 Dec 2021 11:30:41: 4000000 INFO @ Sat, 11 Dec 2021 11:30:44: 10000000 INFO @ Sat, 11 Dec 2021 11:30:44: 15000000 INFO @ Sat, 11 Dec 2021 11:30:47: 5000000 INFO @ Sat, 11 Dec 2021 11:30:50: 11000000 INFO @ Sat, 11 Dec 2021 11:30:50: 16000000 INFO @ Sat, 11 Dec 2021 11:30:54: 6000000 INFO @ Sat, 11 Dec 2021 11:30:56: 12000000 INFO @ Sat, 11 Dec 2021 11:30:56: 17000000 INFO @ Sat, 11 Dec 2021 11:30:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:30:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:30:56: #1 total tags in treatment: 17000668 INFO @ Sat, 11 Dec 2021 11:30:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:30:56: #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 11:30:57: #1 tags after filtering in treatment: 17000668 INFO @ Sat, 11 Dec 2021 11:30:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:30:57: #1 finished! INFO @ Sat, 11 Dec 2021 11:30:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:30:58: #2 number of paired peaks: 450 WARNING @ Sat, 11 Dec 2021 11:30:58: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Sat, 11 Dec 2021 11:30:58: start model_add_line... INFO @ Sat, 11 Dec 2021 11:30:58: start X-correlation... INFO @ Sat, 11 Dec 2021 11:30:58: end of X-cor INFO @ Sat, 11 Dec 2021 11:30:58: #2 finished! INFO @ Sat, 11 Dec 2021 11:30:58: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 11:30:58: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 11 Dec 2021 11:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.05_model.r WARNING @ Sat, 11 Dec 2021 11:30:58: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:30:58: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 11 Dec 2021 11:30:58: #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 11:30:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:31:00: 7000000 INFO @ Sat, 11 Dec 2021 11:31:02: 13000000 INFO @ Sat, 11 Dec 2021 11:31:06: 8000000 INFO @ Sat, 11 Dec 2021 11:31:08: 14000000 INFO @ Sat, 11 Dec 2021 11:31:12: 9000000 INFO @ Sat, 11 Dec 2021 11:31:14: 15000000 INFO @ Sat, 11 Dec 2021 11:31:18: 10000000 INFO @ Sat, 11 Dec 2021 11:31:20: 16000000 INFO @ Sat, 11 Dec 2021 11:31:24: 11000000 INFO @ Sat, 11 Dec 2021 11:31:26: 17000000 INFO @ Sat, 11 Dec 2021 11:31:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:31:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:31:26: #1 total tags in treatment: 17000668 INFO @ Sat, 11 Dec 2021 11:31:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:31:26: #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 11:31:26: #1 tags after filtering in treatment: 17000668 INFO @ Sat, 11 Dec 2021 11:31:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:31:26: #1 finished! INFO @ Sat, 11 Dec 2021 11:31:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:31:27: #2 number of paired peaks: 450 WARNING @ Sat, 11 Dec 2021 11:31:27: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Sat, 11 Dec 2021 11:31:27: start model_add_line... INFO @ Sat, 11 Dec 2021 11:31:27: start X-correlation... INFO @ Sat, 11 Dec 2021 11:31:27: end of X-cor INFO @ Sat, 11 Dec 2021 11:31:27: #2 finished! INFO @ Sat, 11 Dec 2021 11:31:27: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 11:31:27: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 11 Dec 2021 11:31:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.10_model.r WARNING @ Sat, 11 Dec 2021 11:31:27: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:31:27: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 11 Dec 2021 11:31:27: #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 11:31:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:31:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:31:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:31:30: 12000000 INFO @ Sat, 11 Dec 2021 11:31:35: 13000000 INFO @ Sat, 11 Dec 2021 11:31:41: 14000000 INFO @ Sat, 11 Dec 2021 11:31:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:31:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:31:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.05_summits.bed INFO @ Sat, 11 Dec 2021 11:31:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3286 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:31:46: 15000000 INFO @ Sat, 11 Dec 2021 11:31:52: 16000000 INFO @ Sat, 11 Dec 2021 11:31:57: 17000000 INFO @ Sat, 11 Dec 2021 11:31:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:31:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:31:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:31:58: #1 total tags in treatment: 17000668 INFO @ Sat, 11 Dec 2021 11:31:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:31:58: #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 11:31:58: #1 tags after filtering in treatment: 17000668 INFO @ Sat, 11 Dec 2021 11:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:31:58: #1 finished! INFO @ Sat, 11 Dec 2021 11:31:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:31:59: #2 number of paired peaks: 450 WARNING @ Sat, 11 Dec 2021 11:31:59: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Sat, 11 Dec 2021 11:31:59: start model_add_line... INFO @ Sat, 11 Dec 2021 11:31:59: start X-correlation... INFO @ Sat, 11 Dec 2021 11:31:59: end of X-cor INFO @ Sat, 11 Dec 2021 11:31:59: #2 finished! INFO @ Sat, 11 Dec 2021 11:31:59: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 11:31:59: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 11 Dec 2021 11:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.20_model.r WARNING @ Sat, 11 Dec 2021 11:31:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:31:59: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 11 Dec 2021 11:31:59: #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 11:31:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:31:59: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.10_summits.bed INFO @ Sat, 11 Dec 2021 11:32:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2209 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:32:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:32:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:32:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:32:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986144/SRX9986144.20_summits.bed INFO @ Sat, 11 Dec 2021 11:32:46: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1059 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。