Job ID = 14167054 SRX = SRX9343228 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24218711 spots for SRR12877204/SRR12877204.sra Written 24218711 spots for SRR12877204/SRR12877204.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167524 ("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: 00:32:27 24218711 reads; of these: 24218711 (100.00%) were paired; of these: 7292388 (30.11%) aligned concordantly 0 times 14144897 (58.40%) aligned concordantly exactly 1 time 2781426 (11.48%) aligned concordantly >1 times ---- 7292388 pairs aligned concordantly 0 times; of these: 1975666 (27.09%) aligned discordantly 1 time ---- 5316722 pairs aligned 0 times concordantly or discordantly; of these: 10633444 mates make up the pairs; of these: 9297305 (87.43%) aligned 0 times 605089 (5.69%) aligned exactly 1 time 731050 (6.88%) aligned >1 times 80.81% overall alignment rate Time searching: 00:32:27 Overall time: 00:32:27 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 16 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] 1331561 / 18782110 = 0.0709 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 10:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.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 10:11:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:11:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:11:28: 1000000 INFO @ Fri, 10 Dec 2021 10:11:36: 2000000 INFO @ Fri, 10 Dec 2021 10:11:43: 3000000 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 10:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.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 10:11:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:11:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:11:51: 4000000 INFO @ Fri, 10 Dec 2021 10:11:58: 1000000 INFO @ Fri, 10 Dec 2021 10:12:00: 5000000 INFO @ Fri, 10 Dec 2021 10:12:06: 2000000 INFO @ Fri, 10 Dec 2021 10:12:09: 6000000 INFO @ Fri, 10 Dec 2021 10:12:14: 3000000 INFO @ Fri, 10 Dec 2021 10:12:18: 7000000 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 10:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.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 10:12:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:12:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:12:22: 4000000 INFO @ Fri, 10 Dec 2021 10:12:27: 8000000 INFO @ Fri, 10 Dec 2021 10:12:29: 1000000 INFO @ Fri, 10 Dec 2021 10:12:30: 5000000 INFO @ Fri, 10 Dec 2021 10:12:36: 9000000 INFO @ Fri, 10 Dec 2021 10:12:38: 6000000 INFO @ Fri, 10 Dec 2021 10:12:38: 2000000 INFO @ Fri, 10 Dec 2021 10:12:45: 10000000 INFO @ Fri, 10 Dec 2021 10:12:46: 7000000 INFO @ Fri, 10 Dec 2021 10:12:47: 3000000 INFO @ Fri, 10 Dec 2021 10:12:54: 11000000 INFO @ Fri, 10 Dec 2021 10:12:54: 8000000 INFO @ Fri, 10 Dec 2021 10:12:56: 4000000 INFO @ Fri, 10 Dec 2021 10:13:02: 9000000 INFO @ Fri, 10 Dec 2021 10:13:03: 12000000 INFO @ Fri, 10 Dec 2021 10:13:06: 5000000 INFO @ Fri, 10 Dec 2021 10:13:10: 10000000 INFO @ Fri, 10 Dec 2021 10:13:11: 13000000 INFO @ Fri, 10 Dec 2021 10:13:15: 6000000 INFO @ Fri, 10 Dec 2021 10:13:18: 11000000 INFO @ Fri, 10 Dec 2021 10:13:20: 14000000 INFO @ Fri, 10 Dec 2021 10:13:24: 7000000 INFO @ Fri, 10 Dec 2021 10:13:26: 12000000 INFO @ Fri, 10 Dec 2021 10:13:29: 15000000 INFO @ Fri, 10 Dec 2021 10:13:33: 8000000 INFO @ Fri, 10 Dec 2021 10:13:34: 13000000 INFO @ Fri, 10 Dec 2021 10:13:38: 16000000 INFO @ Fri, 10 Dec 2021 10:13:42: 9000000 INFO @ Fri, 10 Dec 2021 10:13:42: 14000000 INFO @ Fri, 10 Dec 2021 10:13:46: 17000000 INFO @ Fri, 10 Dec 2021 10:13:50: 15000000 INFO @ Fri, 10 Dec 2021 10:13:51: 10000000 INFO @ Fri, 10 Dec 2021 10:13:55: 18000000 INFO @ Fri, 10 Dec 2021 10:13:59: 16000000 INFO @ Fri, 10 Dec 2021 10:14:00: 11000000 INFO @ Fri, 10 Dec 2021 10:14:04: 19000000 INFO @ Fri, 10 Dec 2021 10:14:07: 17000000 INFO @ Fri, 10 Dec 2021 10:14:09: 12000000 INFO @ Fri, 10 Dec 2021 10:14:12: 20000000 INFO @ Fri, 10 Dec 2021 10:14:15: 18000000 INFO @ Fri, 10 Dec 2021 10:14:18: 13000000 INFO @ Fri, 10 Dec 2021 10:14:21: 21000000 INFO @ Fri, 10 Dec 2021 10:14:23: 19000000 INFO @ Fri, 10 Dec 2021 10:14:27: 14000000 INFO @ Fri, 10 Dec 2021 10:14:30: 22000000 INFO @ Fri, 10 Dec 2021 10:14:30: 20000000 INFO @ Fri, 10 Dec 2021 10:14:36: 15000000 INFO @ Fri, 10 Dec 2021 10:14:38: 23000000 INFO @ Fri, 10 Dec 2021 10:14:38: 21000000 INFO @ Fri, 10 Dec 2021 10:14:45: 16000000 INFO @ Fri, 10 Dec 2021 10:14:46: 22000000 INFO @ Fri, 10 Dec 2021 10:14:47: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:14:54: 17000000 INFO @ Fri, 10 Dec 2021 10:14:54: 23000000 INFO @ Fri, 10 Dec 2021 10:14:56: 25000000 INFO @ Fri, 10 Dec 2021 10:15:02: 24000000 INFO @ Fri, 10 Dec 2021 10:15:03: 18000000 INFO @ Fri, 10 Dec 2021 10:15:05: 26000000 INFO @ Fri, 10 Dec 2021 10:15:10: 25000000 INFO @ Fri, 10 Dec 2021 10:15:12: 19000000 INFO @ Fri, 10 Dec 2021 10:15:14: 27000000 INFO @ Fri, 10 Dec 2021 10:15:18: 26000000 INFO @ Fri, 10 Dec 2021 10:15:21: 20000000 INFO @ Fri, 10 Dec 2021 10:15:23: 28000000 INFO @ Fri, 10 Dec 2021 10:15:26: 27000000 INFO @ Fri, 10 Dec 2021 10:15:29: 21000000 INFO @ Fri, 10 Dec 2021 10:15:31: 29000000 INFO @ Fri, 10 Dec 2021 10:15:34: 28000000 INFO @ Fri, 10 Dec 2021 10:15:38: 22000000 INFO @ Fri, 10 Dec 2021 10:15:41: 30000000 INFO @ Fri, 10 Dec 2021 10:15:42: 29000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:15:47: 23000000 INFO @ Fri, 10 Dec 2021 10:15:50: 31000000 INFO @ Fri, 10 Dec 2021 10:15:50: 30000000 INFO @ Fri, 10 Dec 2021 10:15:56: 24000000 INFO @ Fri, 10 Dec 2021 10:15:58: 31000000 INFO @ Fri, 10 Dec 2021 10:15:59: 32000000 INFO @ Fri, 10 Dec 2021 10:16:05: 25000000 INFO @ Fri, 10 Dec 2021 10:16:07: 32000000 INFO @ Fri, 10 Dec 2021 10:16:08: 33000000 INFO @ Fri, 10 Dec 2021 10:16:14: 26000000 INFO @ Fri, 10 Dec 2021 10:16:15: 33000000 INFO @ Fri, 10 Dec 2021 10:16:17: 34000000 INFO @ Fri, 10 Dec 2021 10:16:22: 27000000 INFO @ Fri, 10 Dec 2021 10:16:23: 34000000 INFO @ Fri, 10 Dec 2021 10:16:26: 35000000 INFO @ Fri, 10 Dec 2021 10:16:31: 35000000 INFO @ Fri, 10 Dec 2021 10:16:31: 28000000 INFO @ Fri, 10 Dec 2021 10:16:35: 36000000 INFO @ Fri, 10 Dec 2021 10:16:39: 36000000 INFO @ Fri, 10 Dec 2021 10:16:39: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:16:39: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:16:39: #1 total tags in treatment: 15715087 INFO @ Fri, 10 Dec 2021 10:16:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:16:39: #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 10:16:39: #1 tags after filtering in treatment: 12281801 INFO @ Fri, 10 Dec 2021 10:16:39: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 10 Dec 2021 10:16:39: #1 finished! INFO @ Fri, 10 Dec 2021 10:16:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:16:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:16:40: #2 number of paired peaks: 474 WARNING @ Fri, 10 Dec 2021 10:16:40: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Fri, 10 Dec 2021 10:16:40: start model_add_line... INFO @ Fri, 10 Dec 2021 10:16:40: 29000000 INFO @ Fri, 10 Dec 2021 10:16:40: start X-correlation... INFO @ Fri, 10 Dec 2021 10:16:40: end of X-cor INFO @ Fri, 10 Dec 2021 10:16:40: #2 finished! INFO @ Fri, 10 Dec 2021 10:16:40: #2 predicted fragment length is 83 bps INFO @ Fri, 10 Dec 2021 10:16:40: #2 alternative fragment length(s) may be 4,83 bps INFO @ Fri, 10 Dec 2021 10:16:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.05_model.r WARNING @ Fri, 10 Dec 2021 10:16:40: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:16:40: #2 You may need to consider one of the other alternative d(s): 4,83 WARNING @ Fri, 10 Dec 2021 10:16:40: #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 10:16:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:16:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:16:43: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:16:43: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:16:43: #1 total tags in treatment: 15715087 INFO @ Fri, 10 Dec 2021 10:16:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:16:43: #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 10:16:43: #1 tags after filtering in treatment: 12281801 INFO @ Fri, 10 Dec 2021 10:16:43: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 10 Dec 2021 10:16:43: #1 finished! INFO @ Fri, 10 Dec 2021 10:16:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:16:44: #2 number of paired peaks: 474 WARNING @ Fri, 10 Dec 2021 10:16:44: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Fri, 10 Dec 2021 10:16:44: start model_add_line... INFO @ Fri, 10 Dec 2021 10:16:44: start X-correlation... INFO @ Fri, 10 Dec 2021 10:16:44: end of X-cor INFO @ Fri, 10 Dec 2021 10:16:44: #2 finished! INFO @ Fri, 10 Dec 2021 10:16:44: #2 predicted fragment length is 83 bps INFO @ Fri, 10 Dec 2021 10:16:44: #2 alternative fragment length(s) may be 4,83 bps INFO @ Fri, 10 Dec 2021 10:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.10_model.r WARNING @ Fri, 10 Dec 2021 10:16:44: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:16:44: #2 You may need to consider one of the other alternative d(s): 4,83 WARNING @ Fri, 10 Dec 2021 10:16:44: #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 10:16:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:16:48: 30000000 INFO @ Fri, 10 Dec 2021 10:16:56: 31000000 INFO @ Fri, 10 Dec 2021 10:17:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:17:04: 32000000 INFO @ Fri, 10 Dec 2021 10:17:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:17:12: 33000000 INFO @ Fri, 10 Dec 2021 10:17:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:17:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:17:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.05_summits.bed INFO @ Fri, 10 Dec 2021 10:17:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12377 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:17:20: 34000000 INFO @ Fri, 10 Dec 2021 10:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.10_summits.bed INFO @ Fri, 10 Dec 2021 10:17:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5404 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:17:27: 35000000 INFO @ Fri, 10 Dec 2021 10:17:35: 36000000 INFO @ Fri, 10 Dec 2021 10:17:39: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:17:39: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:17:39: #1 total tags in treatment: 15715087 INFO @ Fri, 10 Dec 2021 10:17:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:17:39: #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 10:17:39: #1 tags after filtering in treatment: 12281801 INFO @ Fri, 10 Dec 2021 10:17:39: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 10 Dec 2021 10:17:39: #1 finished! INFO @ Fri, 10 Dec 2021 10:17:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:17:40: #2 number of paired peaks: 474 WARNING @ Fri, 10 Dec 2021 10:17:40: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Fri, 10 Dec 2021 10:17:40: start model_add_line... INFO @ Fri, 10 Dec 2021 10:17:40: start X-correlation... INFO @ Fri, 10 Dec 2021 10:17:40: end of X-cor INFO @ Fri, 10 Dec 2021 10:17:40: #2 finished! INFO @ Fri, 10 Dec 2021 10:17:40: #2 predicted fragment length is 83 bps INFO @ Fri, 10 Dec 2021 10:17:40: #2 alternative fragment length(s) may be 4,83 bps INFO @ Fri, 10 Dec 2021 10:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.20_model.r WARNING @ Fri, 10 Dec 2021 10:17:40: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:17:40: #2 You may need to consider one of the other alternative d(s): 4,83 WARNING @ Fri, 10 Dec 2021 10:17:40: #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 10:17:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:18:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:18:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:18:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:18:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9343228/SRX9343228.20_summits.bed INFO @ Fri, 10 Dec 2021 10:18:15: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (749 records, 4 fields): 3 millis CompletedMACS2peakCalling