Job ID = 14171736 SRX = SRX10386229 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17749027 spots for SRR14009294/SRR14009294.sra Written 17749027 spots for SRR14009294/SRR14009294.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172277 ("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: 00:28:50 17749027 reads; of these: 17749027 (100.00%) were paired; of these: 5967587 (33.62%) aligned concordantly 0 times 7060558 (39.78%) aligned concordantly exactly 1 time 4720882 (26.60%) aligned concordantly >1 times ---- 5967587 pairs aligned concordantly 0 times; of these: 121719 (2.04%) aligned discordantly 1 time ---- 5845868 pairs aligned 0 times concordantly or discordantly; of these: 11691736 mates make up the pairs; of these: 11279379 (96.47%) aligned 0 times 221232 (1.89%) aligned exactly 1 time 191125 (1.63%) aligned >1 times 68.23% overall alignment rate Time searching: 00:28:50 Overall time: 00:28:50 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2169762 / 11848796 = 0.1831 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 13:14:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.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 13:14:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:14:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:14:36: 1000000 INFO @ Sat, 11 Dec 2021 13:14:41: 2000000 INFO @ Sat, 11 Dec 2021 13:14:46: 3000000 INFO @ Sat, 11 Dec 2021 13:14:51: 4000000 INFO @ Sat, 11 Dec 2021 13:14:57: 5000000 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 13:15:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.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 13:15:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:15:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:15:02: 6000000 INFO @ Sat, 11 Dec 2021 13:15:08: 7000000 INFO @ Sat, 11 Dec 2021 13:15:09: 1000000 INFO @ Sat, 11 Dec 2021 13:15:14: 8000000 INFO @ Sat, 11 Dec 2021 13:15:16: 2000000 INFO @ Sat, 11 Dec 2021 13:15:21: 9000000 INFO @ Sat, 11 Dec 2021 13:15:23: 3000000 INFO @ Sat, 11 Dec 2021 13:15:27: 10000000 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 13:15:31: 4000000 INFO @ Sat, 11 Dec 2021 13:15:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.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 13:15:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:15:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:15:34: 11000000 INFO @ Sat, 11 Dec 2021 13:15:38: 1000000 INFO @ Sat, 11 Dec 2021 13:15:38: 5000000 INFO @ Sat, 11 Dec 2021 13:15:40: 12000000 INFO @ Sat, 11 Dec 2021 13:15:44: 2000000 INFO @ Sat, 11 Dec 2021 13:15:45: 6000000 INFO @ Sat, 11 Dec 2021 13:15:46: 13000000 INFO @ Sat, 11 Dec 2021 13:15:50: 3000000 INFO @ Sat, 11 Dec 2021 13:15:53: 7000000 INFO @ Sat, 11 Dec 2021 13:15:53: 14000000 INFO @ Sat, 11 Dec 2021 13:15:57: 4000000 INFO @ Sat, 11 Dec 2021 13:15:59: 15000000 INFO @ Sat, 11 Dec 2021 13:16:00: 8000000 INFO @ Sat, 11 Dec 2021 13:16:03: 5000000 INFO @ Sat, 11 Dec 2021 13:16:06: 16000000 INFO @ Sat, 11 Dec 2021 13:16:08: 9000000 INFO @ Sat, 11 Dec 2021 13:16:10: 6000000 INFO @ Sat, 11 Dec 2021 13:16:12: 17000000 INFO @ Sat, 11 Dec 2021 13:16:15: 10000000 INFO @ Sat, 11 Dec 2021 13:16:16: 7000000 INFO @ Sat, 11 Dec 2021 13:16:19: 18000000 INFO @ Sat, 11 Dec 2021 13:16:22: 11000000 INFO @ Sat, 11 Dec 2021 13:16:22: 8000000 INFO @ Sat, 11 Dec 2021 13:16:25: 19000000 INFO @ Sat, 11 Dec 2021 13:16:29: 9000000 INFO @ Sat, 11 Dec 2021 13:16:30: 12000000 INFO @ Sat, 11 Dec 2021 13:16:31: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:16:31: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:16:31: #1 total tags in treatment: 9619584 INFO @ Sat, 11 Dec 2021 13:16:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:16:31: #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 13:16:31: #1 tags after filtering in treatment: 7910466 INFO @ Sat, 11 Dec 2021 13:16:31: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 13:16:31: #1 finished! INFO @ Sat, 11 Dec 2021 13:16:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:16:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:16:32: #2 number of paired peaks: 690 WARNING @ Sat, 11 Dec 2021 13:16:32: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sat, 11 Dec 2021 13:16:32: start model_add_line... INFO @ Sat, 11 Dec 2021 13:16:32: start X-correlation... INFO @ Sat, 11 Dec 2021 13:16:32: end of X-cor INFO @ Sat, 11 Dec 2021 13:16:32: #2 finished! INFO @ Sat, 11 Dec 2021 13:16:32: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 13:16:32: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 13:16:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.05_model.r WARNING @ Sat, 11 Dec 2021 13:16:32: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:16:32: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 13:16:32: #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 13:16:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:16:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:16:35: 10000000 INFO @ Sat, 11 Dec 2021 13:16:37: 13000000 INFO @ Sat, 11 Dec 2021 13:16:41: 11000000 INFO @ Sat, 11 Dec 2021 13:16:44: 14000000 INFO @ Sat, 11 Dec 2021 13:16:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:16:48: 12000000 INFO @ Sat, 11 Dec 2021 13:16:51: 15000000 INFO @ Sat, 11 Dec 2021 13:16:54: 13000000 INFO @ Sat, 11 Dec 2021 13:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.05_summits.bed INFO @ Sat, 11 Dec 2021 13:16:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3213 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:16:59: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:17:00: 14000000 INFO @ Sat, 11 Dec 2021 13:17:06: 17000000 INFO @ Sat, 11 Dec 2021 13:17:07: 15000000 INFO @ Sat, 11 Dec 2021 13:17:12: 18000000 INFO @ Sat, 11 Dec 2021 13:17:13: 16000000 INFO @ Sat, 11 Dec 2021 13:17:20: 19000000 INFO @ Sat, 11 Dec 2021 13:17:20: 17000000 INFO @ Sat, 11 Dec 2021 13:17:25: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:17:25: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:17:25: #1 total tags in treatment: 9619584 INFO @ Sat, 11 Dec 2021 13:17:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:17:25: #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 13:17:26: #1 tags after filtering in treatment: 7910466 INFO @ Sat, 11 Dec 2021 13:17:26: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 13:17:26: #1 finished! INFO @ Sat, 11 Dec 2021 13:17:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:17:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:17:26: 18000000 INFO @ Sat, 11 Dec 2021 13:17:26: #2 number of paired peaks: 690 WARNING @ Sat, 11 Dec 2021 13:17:26: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sat, 11 Dec 2021 13:17:26: start model_add_line... INFO @ Sat, 11 Dec 2021 13:17:26: start X-correlation... INFO @ Sat, 11 Dec 2021 13:17:26: end of X-cor INFO @ Sat, 11 Dec 2021 13:17:26: #2 finished! INFO @ Sat, 11 Dec 2021 13:17:26: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 13:17:26: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 13:17:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.10_model.r WARNING @ Sat, 11 Dec 2021 13:17:26: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:17:26: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 13:17:26: #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 13:17:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:17:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:17:32: 19000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:17:36: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:17:36: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:17:36: #1 total tags in treatment: 9619584 INFO @ Sat, 11 Dec 2021 13:17:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:17:36: #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 13:17:37: #1 tags after filtering in treatment: 7910466 INFO @ Sat, 11 Dec 2021 13:17:37: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 13:17:37: #1 finished! INFO @ Sat, 11 Dec 2021 13:17:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:17:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:17:37: #2 number of paired peaks: 690 WARNING @ Sat, 11 Dec 2021 13:17:37: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sat, 11 Dec 2021 13:17:37: start model_add_line... INFO @ Sat, 11 Dec 2021 13:17:37: start X-correlation... INFO @ Sat, 11 Dec 2021 13:17:37: end of X-cor INFO @ Sat, 11 Dec 2021 13:17:37: #2 finished! INFO @ Sat, 11 Dec 2021 13:17:37: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 13:17:37: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 13:17:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.20_model.r WARNING @ Sat, 11 Dec 2021 13:17:37: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:17:37: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 13:17:37: #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 13:17:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:17:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:17:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:17:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:17:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:17:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.10_summits.bed INFO @ Sat, 11 Dec 2021 13:17:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1642 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:17:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:18:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:18:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:18:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386229/SRX10386229.20_summits.bed INFO @ Sat, 11 Dec 2021 13:18:02: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (822 records, 4 fields): 3 millis CompletedMACS2peakCalling