Job ID = 14170100 SRX = SRX8556253 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 39264446 spots for SRR12024627/SRR12024627.sra Written 39264446 spots for SRR12024627/SRR12024627.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170728 ("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: 00:52:31 39264446 reads; of these: 39264446 (100.00%) were paired; of these: 31601466 (80.48%) aligned concordantly 0 times 5415781 (13.79%) aligned concordantly exactly 1 time 2247199 (5.72%) aligned concordantly >1 times ---- 31601466 pairs aligned concordantly 0 times; of these: 1544949 (4.89%) aligned discordantly 1 time ---- 30056517 pairs aligned 0 times concordantly or discordantly; of these: 60113034 mates make up the pairs; of these: 58143867 (96.72%) aligned 0 times 469416 (0.78%) aligned exactly 1 time 1499751 (2.49%) aligned >1 times 25.96% overall alignment rate Time searching: 00:52:31 Overall time: 00:52:31 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] 1026737 / 9150956 = 0.1122 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 06:23:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.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 06:23:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:23:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:23:43: 1000000 INFO @ Sat, 11 Dec 2021 06:23:49: 2000000 INFO @ Sat, 11 Dec 2021 06:23:56: 3000000 INFO @ Sat, 11 Dec 2021 06:24:03: 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 06:24:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.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 06:24:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:24:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:24:10: 5000000 INFO @ Sat, 11 Dec 2021 06:24:13: 1000000 INFO @ Sat, 11 Dec 2021 06:24:18: 6000000 INFO @ Sat, 11 Dec 2021 06:24:20: 2000000 INFO @ Sat, 11 Dec 2021 06:24:25: 7000000 INFO @ Sat, 11 Dec 2021 06:24:28: 3000000 INFO @ Sat, 11 Dec 2021 06:24:33: 8000000 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 06:24:35: 4000000 INFO @ Sat, 11 Dec 2021 06:24:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.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 06:24:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:24:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:24:40: 9000000 INFO @ Sat, 11 Dec 2021 06:24:43: 5000000 INFO @ Sat, 11 Dec 2021 06:24:44: 1000000 INFO @ Sat, 11 Dec 2021 06:24:48: 10000000 INFO @ Sat, 11 Dec 2021 06:24:51: 6000000 INFO @ Sat, 11 Dec 2021 06:24:52: 2000000 INFO @ Sat, 11 Dec 2021 06:24:56: 11000000 INFO @ Sat, 11 Dec 2021 06:24:58: 7000000 INFO @ Sat, 11 Dec 2021 06:24:59: 3000000 INFO @ Sat, 11 Dec 2021 06:25:04: 12000000 INFO @ Sat, 11 Dec 2021 06:25:06: 8000000 INFO @ Sat, 11 Dec 2021 06:25:07: 4000000 INFO @ Sat, 11 Dec 2021 06:25:11: 13000000 INFO @ Sat, 11 Dec 2021 06:25:14: 9000000 INFO @ Sat, 11 Dec 2021 06:25:15: 5000000 INFO @ Sat, 11 Dec 2021 06:25:19: 14000000 INFO @ Sat, 11 Dec 2021 06:25:21: 10000000 INFO @ Sat, 11 Dec 2021 06:25:22: 6000000 INFO @ Sat, 11 Dec 2021 06:25:26: 15000000 INFO @ Sat, 11 Dec 2021 06:25:29: 11000000 INFO @ Sat, 11 Dec 2021 06:25:30: 7000000 INFO @ Sat, 11 Dec 2021 06:25:34: 16000000 INFO @ Sat, 11 Dec 2021 06:25:37: 12000000 INFO @ Sat, 11 Dec 2021 06:25:38: 8000000 INFO @ Sat, 11 Dec 2021 06:25:42: 17000000 INFO @ Sat, 11 Dec 2021 06:25:44: 13000000 INFO @ Sat, 11 Dec 2021 06:25:45: 9000000 INFO @ Sat, 11 Dec 2021 06:25:49: 18000000 INFO @ Sat, 11 Dec 2021 06:25:51: 14000000 INFO @ Sat, 11 Dec 2021 06:25:52: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:25:52: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:25:52: #1 total tags in treatment: 6738774 INFO @ Sat, 11 Dec 2021 06:25:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:25:52: #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 06:25:52: #1 tags after filtering in treatment: 5918627 INFO @ Sat, 11 Dec 2021 06:25:52: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:25:52: #1 finished! INFO @ Sat, 11 Dec 2021 06:25:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:25:53: #2 number of paired peaks: 402 WARNING @ Sat, 11 Dec 2021 06:25:53: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Sat, 11 Dec 2021 06:25:53: start model_add_line... INFO @ Sat, 11 Dec 2021 06:25:53: start X-correlation... INFO @ Sat, 11 Dec 2021 06:25:53: end of X-cor INFO @ Sat, 11 Dec 2021 06:25:53: #2 finished! INFO @ Sat, 11 Dec 2021 06:25:53: #2 predicted fragment length is 207 bps INFO @ Sat, 11 Dec 2021 06:25:53: #2 alternative fragment length(s) may be 207 bps INFO @ Sat, 11 Dec 2021 06:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.05_model.r WARNING @ Sat, 11 Dec 2021 06:25:53: #2 Since the d (207) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:25:53: #2 You may need to consider one of the other alternative d(s): 207 WARNING @ Sat, 11 Dec 2021 06:25:53: #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 06:25:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:25:53: 10000000 INFO @ Sat, 11 Dec 2021 06:25:59: 15000000 INFO @ Sat, 11 Dec 2021 06:26:00: 11000000 INFO @ Sat, 11 Dec 2021 06:26:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:26:06: 16000000 INFO @ Sat, 11 Dec 2021 06:26:08: 12000000 INFO @ Sat, 11 Dec 2021 06:26:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:26:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:26:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.05_summits.bed INFO @ Sat, 11 Dec 2021 06:26:12: Done! INFO @ Sat, 11 Dec 2021 06:26:14: 17000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2190 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:26:15: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:26:22: 18000000 INFO @ Sat, 11 Dec 2021 06:26:22: 14000000 INFO @ Sat, 11 Dec 2021 06:26:24: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:26:24: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:26:24: #1 total tags in treatment: 6738774 INFO @ Sat, 11 Dec 2021 06:26:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:26:24: #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 06:26:24: #1 tags after filtering in treatment: 5918627 INFO @ Sat, 11 Dec 2021 06:26:24: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:26:24: #1 finished! INFO @ Sat, 11 Dec 2021 06:26:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:26:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:26:25: #2 number of paired peaks: 402 WARNING @ Sat, 11 Dec 2021 06:26:25: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Sat, 11 Dec 2021 06:26:25: start model_add_line... INFO @ Sat, 11 Dec 2021 06:26:25: start X-correlation... INFO @ Sat, 11 Dec 2021 06:26:25: end of X-cor INFO @ Sat, 11 Dec 2021 06:26:25: #2 finished! INFO @ Sat, 11 Dec 2021 06:26:25: #2 predicted fragment length is 207 bps INFO @ Sat, 11 Dec 2021 06:26:25: #2 alternative fragment length(s) may be 207 bps INFO @ Sat, 11 Dec 2021 06:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.10_model.r WARNING @ Sat, 11 Dec 2021 06:26:25: #2 Since the d (207) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:26:25: #2 You may need to consider one of the other alternative d(s): 207 WARNING @ Sat, 11 Dec 2021 06:26:25: #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 06:26:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:26:30: 15000000 INFO @ Sat, 11 Dec 2021 06:26:37: 16000000 INFO @ Sat, 11 Dec 2021 06:26:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:26:44: 17000000 INFO @ Sat, 11 Dec 2021 06:26:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:26:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:26:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.10_summits.bed INFO @ Sat, 11 Dec 2021 06:26:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (810 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:26:52: 18000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:26:54: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:26:54: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:26:54: #1 total tags in treatment: 6738774 INFO @ Sat, 11 Dec 2021 06:26:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:26:54: #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 06:26:54: #1 tags after filtering in treatment: 5918627 INFO @ Sat, 11 Dec 2021 06:26:54: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:26:54: #1 finished! INFO @ Sat, 11 Dec 2021 06:26:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:26:55: #2 number of paired peaks: 402 WARNING @ Sat, 11 Dec 2021 06:26:55: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Sat, 11 Dec 2021 06:26:55: start model_add_line... INFO @ Sat, 11 Dec 2021 06:26:55: start X-correlation... INFO @ Sat, 11 Dec 2021 06:26:55: end of X-cor INFO @ Sat, 11 Dec 2021 06:26:55: #2 finished! INFO @ Sat, 11 Dec 2021 06:26:55: #2 predicted fragment length is 207 bps INFO @ Sat, 11 Dec 2021 06:26:55: #2 alternative fragment length(s) may be 207 bps INFO @ Sat, 11 Dec 2021 06:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.20_model.r WARNING @ Sat, 11 Dec 2021 06:26:55: #2 Since the d (207) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:26:55: #2 You may need to consider one of the other alternative d(s): 207 WARNING @ Sat, 11 Dec 2021 06:26:55: #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 06:26:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:27:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:27:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:27:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:27:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556253/SRX8556253.20_summits.bed INFO @ Sat, 11 Dec 2021 06:27:14: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (379 records, 4 fields): 2 millis CompletedMACS2peakCalling