Job ID = 14171528 SRX = SRX10386203 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24682667 spots for SRR14009268/SRR14009268.sra Written 24682667 spots for SRR14009268/SRR14009268.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172312 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:19:34 24682667 reads; of these: 24682667 (100.00%) were paired; of these: 3901758 (15.81%) aligned concordantly 0 times 13392976 (54.26%) aligned concordantly exactly 1 time 7387933 (29.93%) aligned concordantly >1 times ---- 3901758 pairs aligned concordantly 0 times; of these: 474433 (12.16%) aligned discordantly 1 time ---- 3427325 pairs aligned 0 times concordantly or discordantly; of these: 6854650 mates make up the pairs; of these: 5680511 (82.87%) aligned 0 times 633178 (9.24%) aligned exactly 1 time 540961 (7.89%) aligned >1 times 88.49% overall alignment rate Time searching: 01:19:35 Overall time: 01:19:35 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 20 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] 3098598 / 21205474 = 0.1461 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 13:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.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 13:34:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:34:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:34:47: 1000000 INFO @ Sat, 11 Dec 2021 13:34:54: 2000000 INFO @ Sat, 11 Dec 2021 13:35:01: 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 @ Sat, 11 Dec 2021 13:35:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.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 13:35:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:35:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:35:09: 4000000 INFO @ Sat, 11 Dec 2021 13:35:16: 5000000 INFO @ Sat, 11 Dec 2021 13:35:17: 1000000 INFO @ Sat, 11 Dec 2021 13:35:23: 6000000 INFO @ Sat, 11 Dec 2021 13:35:25: 2000000 INFO @ Sat, 11 Dec 2021 13:35:30: 7000000 INFO @ Sat, 11 Dec 2021 13:35:34: 3000000 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 13:35:37: 8000000 INFO @ Sat, 11 Dec 2021 13:35:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.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 13:35:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:35:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:35:43: 4000000 INFO @ Sat, 11 Dec 2021 13:35:44: 9000000 INFO @ Sat, 11 Dec 2021 13:35:47: 1000000 INFO @ Sat, 11 Dec 2021 13:35:51: 10000000 INFO @ Sat, 11 Dec 2021 13:35:53: 5000000 INFO @ Sat, 11 Dec 2021 13:35:55: 2000000 INFO @ Sat, 11 Dec 2021 13:35:58: 11000000 INFO @ Sat, 11 Dec 2021 13:36:02: 6000000 INFO @ Sat, 11 Dec 2021 13:36:04: 3000000 INFO @ Sat, 11 Dec 2021 13:36:05: 12000000 INFO @ Sat, 11 Dec 2021 13:36:11: 7000000 INFO @ Sat, 11 Dec 2021 13:36:12: 13000000 INFO @ Sat, 11 Dec 2021 13:36:13: 4000000 INFO @ Sat, 11 Dec 2021 13:36:19: 14000000 INFO @ Sat, 11 Dec 2021 13:36:20: 8000000 INFO @ Sat, 11 Dec 2021 13:36:22: 5000000 INFO @ Sat, 11 Dec 2021 13:36:26: 15000000 INFO @ Sat, 11 Dec 2021 13:36:29: 9000000 INFO @ Sat, 11 Dec 2021 13:36:31: 6000000 INFO @ Sat, 11 Dec 2021 13:36:34: 16000000 INFO @ Sat, 11 Dec 2021 13:36:38: 10000000 INFO @ Sat, 11 Dec 2021 13:36:40: 7000000 INFO @ Sat, 11 Dec 2021 13:36:41: 17000000 INFO @ Sat, 11 Dec 2021 13:36:47: 11000000 INFO @ Sat, 11 Dec 2021 13:36:48: 18000000 INFO @ Sat, 11 Dec 2021 13:36:49: 8000000 INFO @ Sat, 11 Dec 2021 13:36:55: 19000000 INFO @ Sat, 11 Dec 2021 13:36:56: 12000000 INFO @ Sat, 11 Dec 2021 13:36:58: 9000000 INFO @ Sat, 11 Dec 2021 13:37:02: 20000000 INFO @ Sat, 11 Dec 2021 13:37:05: 13000000 INFO @ Sat, 11 Dec 2021 13:37:07: 10000000 INFO @ Sat, 11 Dec 2021 13:37:09: 21000000 INFO @ Sat, 11 Dec 2021 13:37:15: 14000000 INFO @ Sat, 11 Dec 2021 13:37:16: 22000000 INFO @ Sat, 11 Dec 2021 13:37:16: 11000000 INFO @ Sat, 11 Dec 2021 13:37:23: 23000000 INFO @ Sat, 11 Dec 2021 13:37:24: 15000000 INFO @ Sat, 11 Dec 2021 13:37:25: 12000000 INFO @ Sat, 11 Dec 2021 13:37:31: 24000000 INFO @ Sat, 11 Dec 2021 13:37:33: 16000000 INFO @ Sat, 11 Dec 2021 13:37:34: 13000000 INFO @ Sat, 11 Dec 2021 13:37:39: 25000000 INFO @ Sat, 11 Dec 2021 13:37:42: 17000000 INFO @ Sat, 11 Dec 2021 13:37:43: 14000000 INFO @ Sat, 11 Dec 2021 13:37:47: 26000000 INFO @ Sat, 11 Dec 2021 13:37:51: 18000000 INFO @ Sat, 11 Dec 2021 13:37:52: 15000000 INFO @ Sat, 11 Dec 2021 13:37:54: 27000000 INFO @ Sat, 11 Dec 2021 13:38:00: 19000000 INFO @ Sat, 11 Dec 2021 13:38:01: 28000000 INFO @ Sat, 11 Dec 2021 13:38:01: 16000000 INFO @ Sat, 11 Dec 2021 13:38:09: 29000000 INFO @ Sat, 11 Dec 2021 13:38:09: 20000000 INFO @ Sat, 11 Dec 2021 13:38:10: 17000000 INFO @ Sat, 11 Dec 2021 13:38:16: 30000000 INFO @ Sat, 11 Dec 2021 13:38:18: 21000000 INFO @ Sat, 11 Dec 2021 13:38:19: 18000000 INFO @ Sat, 11 Dec 2021 13:38:23: 31000000 INFO @ Sat, 11 Dec 2021 13:38:27: 22000000 INFO @ Sat, 11 Dec 2021 13:38:28: 19000000 INFO @ Sat, 11 Dec 2021 13:38:30: 32000000 INFO @ Sat, 11 Dec 2021 13:38:36: 23000000 INFO @ Sat, 11 Dec 2021 13:38:37: 20000000 INFO @ Sat, 11 Dec 2021 13:38:37: 33000000 INFO @ Sat, 11 Dec 2021 13:38:45: 34000000 INFO @ Sat, 11 Dec 2021 13:38:45: 24000000 INFO @ Sat, 11 Dec 2021 13:38:46: 21000000 INFO @ Sat, 11 Dec 2021 13:38:52: 35000000 INFO @ Sat, 11 Dec 2021 13:38:54: 25000000 INFO @ Sat, 11 Dec 2021 13:38:55: 22000000 INFO @ Sat, 11 Dec 2021 13:38:59: 36000000 INFO @ Sat, 11 Dec 2021 13:39:03: 23000000 INFO @ Sat, 11 Dec 2021 13:39:04: 26000000 INFO @ Sat, 11 Dec 2021 13:39:06: 37000000 INFO @ Sat, 11 Dec 2021 13:39:10: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 13:39:10: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 13:39:10: #1 total tags in treatment: 17708767 INFO @ Sat, 11 Dec 2021 13:39:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:39:10: #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 13:39:10: #1 tags after filtering in treatment: 14145928 INFO @ Sat, 11 Dec 2021 13:39:10: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 13:39:10: #1 finished! INFO @ Sat, 11 Dec 2021 13:39:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:39:11: #2 number of paired peaks: 191 WARNING @ Sat, 11 Dec 2021 13:39:11: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 11 Dec 2021 13:39:11: start model_add_line... INFO @ Sat, 11 Dec 2021 13:39:11: start X-correlation... INFO @ Sat, 11 Dec 2021 13:39:11: end of X-cor INFO @ Sat, 11 Dec 2021 13:39:11: #2 finished! INFO @ Sat, 11 Dec 2021 13:39:11: #2 predicted fragment length is 97 bps INFO @ Sat, 11 Dec 2021 13:39:11: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 11 Dec 2021 13:39:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.05_model.r WARNING @ Sat, 11 Dec 2021 13:39:11: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:39:11: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 11 Dec 2021 13:39:11: #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 13:39:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:39:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:39:12: 24000000 INFO @ Sat, 11 Dec 2021 13:39:13: 27000000 INFO @ Sat, 11 Dec 2021 13:39:21: 25000000 INFO @ Sat, 11 Dec 2021 13:39:21: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:39:29: 26000000 INFO @ Sat, 11 Dec 2021 13:39:30: 29000000 INFO @ Sat, 11 Dec 2021 13:39:38: 30000000 INFO @ Sat, 11 Dec 2021 13:39:38: 27000000 INFO @ Sat, 11 Dec 2021 13:39:47: 31000000 INFO @ Sat, 11 Dec 2021 13:39:47: 28000000 INFO @ Sat, 11 Dec 2021 13:39:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:39:56: 29000000 INFO @ Sat, 11 Dec 2021 13:39:56: 32000000 INFO @ Sat, 11 Dec 2021 13:40:04: 30000000 INFO @ Sat, 11 Dec 2021 13:40:05: 33000000 INFO @ Sat, 11 Dec 2021 13:40:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:40:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:40:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.05_summits.bed INFO @ Sat, 11 Dec 2021 13:40:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2119 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:40:13: 31000000 INFO @ Sat, 11 Dec 2021 13:40:13: 34000000 INFO @ Sat, 11 Dec 2021 13:40:22: 32000000 INFO @ Sat, 11 Dec 2021 13:40:22: 35000000 INFO @ Sat, 11 Dec 2021 13:40:30: 33000000 INFO @ Sat, 11 Dec 2021 13:40:31: 36000000 INFO @ Sat, 11 Dec 2021 13:40:39: 34000000 INFO @ Sat, 11 Dec 2021 13:40:40: 37000000 INFO @ Sat, 11 Dec 2021 13:40:44: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 13:40:44: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 13:40:44: #1 total tags in treatment: 17708767 INFO @ Sat, 11 Dec 2021 13:40:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:40:44: #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 13:40:45: #1 tags after filtering in treatment: 14145928 INFO @ Sat, 11 Dec 2021 13:40:45: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 13:40:45: #1 finished! INFO @ Sat, 11 Dec 2021 13:40:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:40:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:40:46: #2 number of paired peaks: 191 WARNING @ Sat, 11 Dec 2021 13:40:46: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 11 Dec 2021 13:40:46: start model_add_line... INFO @ Sat, 11 Dec 2021 13:40:46: start X-correlation... INFO @ Sat, 11 Dec 2021 13:40:46: end of X-cor INFO @ Sat, 11 Dec 2021 13:40:46: #2 finished! INFO @ Sat, 11 Dec 2021 13:40:46: #2 predicted fragment length is 97 bps INFO @ Sat, 11 Dec 2021 13:40:46: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 11 Dec 2021 13:40:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.10_model.r WARNING @ Sat, 11 Dec 2021 13:40:46: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:40:46: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 11 Dec 2021 13:40:46: #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 13:40:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:40:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:40:48: 35000000 INFO @ Sat, 11 Dec 2021 13:40:56: 36000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:41:05: 37000000 INFO @ Sat, 11 Dec 2021 13:41:09: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 13:41:09: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 13:41:09: #1 total tags in treatment: 17708767 INFO @ Sat, 11 Dec 2021 13:41:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:41:09: #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 13:41:10: #1 tags after filtering in treatment: 14145928 INFO @ Sat, 11 Dec 2021 13:41:10: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 13:41:10: #1 finished! INFO @ Sat, 11 Dec 2021 13:41:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:41:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:41:11: #2 number of paired peaks: 191 WARNING @ Sat, 11 Dec 2021 13:41:11: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 11 Dec 2021 13:41:11: start model_add_line... INFO @ Sat, 11 Dec 2021 13:41:11: start X-correlation... INFO @ Sat, 11 Dec 2021 13:41:11: end of X-cor INFO @ Sat, 11 Dec 2021 13:41:11: #2 finished! INFO @ Sat, 11 Dec 2021 13:41:11: #2 predicted fragment length is 97 bps INFO @ Sat, 11 Dec 2021 13:41:11: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 11 Dec 2021 13:41:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.20_model.r WARNING @ Sat, 11 Dec 2021 13:41:11: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:41:11: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 11 Dec 2021 13:41:11: #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 13:41:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:41:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:41:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:41:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:41:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:41:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.10_summits.bed INFO @ Sat, 11 Dec 2021 13:41:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1206 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:41:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:42:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:42:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:42:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386203/SRX10386203.20_summits.bed INFO @ Sat, 11 Dec 2021 13:42:10: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (757 records, 4 fields): 4 millis CompletedMACS2peakCalling