Job ID = 14167073 SRX = SRX10412055 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29406694 spots for SRR14035717/SRR14035717.sra Written 29406694 spots for SRR14035717/SRR14035717.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167606 ("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: 00:54:09 29406694 reads; of these: 29406694 (100.00%) were paired; of these: 14991559 (50.98%) aligned concordantly 0 times 12921146 (43.94%) aligned concordantly exactly 1 time 1493989 (5.08%) aligned concordantly >1 times ---- 14991559 pairs aligned concordantly 0 times; of these: 5325289 (35.52%) aligned discordantly 1 time ---- 9666270 pairs aligned 0 times concordantly or discordantly; of these: 19332540 mates make up the pairs; of these: 17058990 (88.24%) aligned 0 times 1256678 (6.50%) aligned exactly 1 time 1016872 (5.26%) aligned >1 times 70.99% overall alignment rate Time searching: 00:54:09 Overall time: 00:54:09 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 32 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] 3903603 / 19675541 = 0.1984 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 10:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.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 10:49:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:49:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:49:18: 1000000 INFO @ Fri, 10 Dec 2021 10:49:25: 2000000 INFO @ Fri, 10 Dec 2021 10:49:33: 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 10:49:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.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 10:49:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:49:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:49:41: 4000000 INFO @ Fri, 10 Dec 2021 10:49:51: 1000000 INFO @ Fri, 10 Dec 2021 10:49:51: 5000000 INFO @ Fri, 10 Dec 2021 10:50:01: 6000000 INFO @ Fri, 10 Dec 2021 10:50:02: 2000000 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 10:50:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.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 10:50:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:50:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:50:11: 7000000 INFO @ Fri, 10 Dec 2021 10:50:14: 3000000 INFO @ Fri, 10 Dec 2021 10:50:21: 1000000 INFO @ Fri, 10 Dec 2021 10:50:22: 8000000 INFO @ Fri, 10 Dec 2021 10:50:26: 4000000 INFO @ Fri, 10 Dec 2021 10:50:32: 9000000 INFO @ Fri, 10 Dec 2021 10:50:33: 2000000 INFO @ Fri, 10 Dec 2021 10:50:38: 5000000 INFO @ Fri, 10 Dec 2021 10:50:42: 10000000 INFO @ Fri, 10 Dec 2021 10:50:44: 3000000 INFO @ Fri, 10 Dec 2021 10:50:49: 6000000 INFO @ Fri, 10 Dec 2021 10:50:53: 11000000 INFO @ Fri, 10 Dec 2021 10:50:56: 4000000 INFO @ Fri, 10 Dec 2021 10:51:01: 7000000 INFO @ Fri, 10 Dec 2021 10:51:03: 12000000 INFO @ Fri, 10 Dec 2021 10:51:07: 5000000 INFO @ Fri, 10 Dec 2021 10:51:13: 8000000 INFO @ Fri, 10 Dec 2021 10:51:13: 13000000 INFO @ Fri, 10 Dec 2021 10:51:19: 6000000 INFO @ Fri, 10 Dec 2021 10:51:24: 14000000 INFO @ Fri, 10 Dec 2021 10:51:25: 9000000 INFO @ Fri, 10 Dec 2021 10:51:30: 7000000 INFO @ Fri, 10 Dec 2021 10:51:34: 15000000 INFO @ Fri, 10 Dec 2021 10:51:37: 10000000 INFO @ Fri, 10 Dec 2021 10:51:42: 8000000 INFO @ Fri, 10 Dec 2021 10:51:44: 16000000 INFO @ Fri, 10 Dec 2021 10:51:49: 11000000 INFO @ Fri, 10 Dec 2021 10:51:53: 9000000 INFO @ Fri, 10 Dec 2021 10:51:55: 17000000 INFO @ Fri, 10 Dec 2021 10:52:01: 12000000 INFO @ Fri, 10 Dec 2021 10:52:05: 10000000 INFO @ Fri, 10 Dec 2021 10:52:05: 18000000 INFO @ Fri, 10 Dec 2021 10:52:13: 13000000 INFO @ Fri, 10 Dec 2021 10:52:15: 19000000 INFO @ Fri, 10 Dec 2021 10:52:17: 11000000 INFO @ Fri, 10 Dec 2021 10:52:24: 14000000 INFO @ Fri, 10 Dec 2021 10:52:25: 20000000 INFO @ Fri, 10 Dec 2021 10:52:28: 12000000 INFO @ Fri, 10 Dec 2021 10:52:35: 21000000 INFO @ Fri, 10 Dec 2021 10:52:36: 15000000 INFO @ Fri, 10 Dec 2021 10:52:40: 13000000 INFO @ Fri, 10 Dec 2021 10:52:45: 22000000 INFO @ Fri, 10 Dec 2021 10:52:48: 16000000 INFO @ Fri, 10 Dec 2021 10:52:52: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:52:55: 23000000 INFO @ Fri, 10 Dec 2021 10:53:00: 17000000 INFO @ Fri, 10 Dec 2021 10:53:03: 15000000 INFO @ Fri, 10 Dec 2021 10:53:05: 24000000 INFO @ Fri, 10 Dec 2021 10:53:12: 18000000 INFO @ Fri, 10 Dec 2021 10:53:15: 16000000 INFO @ Fri, 10 Dec 2021 10:53:15: 25000000 INFO @ Fri, 10 Dec 2021 10:53:23: 19000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:53:26: 26000000 INFO @ Fri, 10 Dec 2021 10:53:27: 17000000 INFO @ Fri, 10 Dec 2021 10:53:35: 20000000 INFO @ Fri, 10 Dec 2021 10:53:36: 27000000 INFO @ Fri, 10 Dec 2021 10:53:38: 18000000 INFO @ Fri, 10 Dec 2021 10:53:46: 28000000 INFO @ Fri, 10 Dec 2021 10:53:46: 21000000 INFO @ Fri, 10 Dec 2021 10:53:50: 19000000 INFO @ Fri, 10 Dec 2021 10:53:57: 29000000 INFO @ Fri, 10 Dec 2021 10:53:58: 22000000 INFO @ Fri, 10 Dec 2021 10:54:01: 20000000 INFO @ Fri, 10 Dec 2021 10:54:07: 30000000 INFO @ Fri, 10 Dec 2021 10:54:09: 23000000 INFO @ Fri, 10 Dec 2021 10:54:13: 21000000 INFO @ Fri, 10 Dec 2021 10:54:17: 31000000 INFO @ Fri, 10 Dec 2021 10:54:20: 24000000 INFO @ Fri, 10 Dec 2021 10:54:24: 22000000 INFO @ Fri, 10 Dec 2021 10:54:28: 32000000 INFO @ Fri, 10 Dec 2021 10:54:32: 25000000 INFO @ Fri, 10 Dec 2021 10:54:35: 23000000 INFO @ Fri, 10 Dec 2021 10:54:38: 33000000 INFO @ Fri, 10 Dec 2021 10:54:43: 26000000 INFO @ Fri, 10 Dec 2021 10:54:46: 24000000 INFO @ Fri, 10 Dec 2021 10:54:48: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 10:54:48: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 10:54:48: #1 total tags in treatment: 11344803 INFO @ Fri, 10 Dec 2021 10:54:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:54:48: #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 10:54:48: #1 tags after filtering in treatment: 6742233 INFO @ Fri, 10 Dec 2021 10:54:48: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 10 Dec 2021 10:54:48: #1 finished! INFO @ Fri, 10 Dec 2021 10:54:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:54:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:54:49: #2 number of paired peaks: 6829 INFO @ Fri, 10 Dec 2021 10:54:49: start model_add_line... INFO @ Fri, 10 Dec 2021 10:54:49: start X-correlation... INFO @ Fri, 10 Dec 2021 10:54:49: end of X-cor INFO @ Fri, 10 Dec 2021 10:54:49: #2 finished! INFO @ Fri, 10 Dec 2021 10:54:49: #2 predicted fragment length is 277 bps INFO @ Fri, 10 Dec 2021 10:54:49: #2 alternative fragment length(s) may be 277 bps INFO @ Fri, 10 Dec 2021 10:54:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.05_model.r WARNING @ Fri, 10 Dec 2021 10:54:49: #2 Since the d (277) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:54:49: #2 You may need to consider one of the other alternative d(s): 277 WARNING @ Fri, 10 Dec 2021 10:54:49: #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 10:54:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:54:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:54:54: 27000000 INFO @ Fri, 10 Dec 2021 10:54:58: 25000000 INFO @ Fri, 10 Dec 2021 10:55:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:55:06: 28000000 INFO @ Fri, 10 Dec 2021 10:55:09: 26000000 INFO @ Fri, 10 Dec 2021 10:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.05_summits.bed INFO @ Fri, 10 Dec 2021 10:55:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9202 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:55:18: 29000000 INFO @ Fri, 10 Dec 2021 10:55:20: 27000000 INFO @ Fri, 10 Dec 2021 10:55:30: 30000000 INFO @ Fri, 10 Dec 2021 10:55:31: 28000000 INFO @ Fri, 10 Dec 2021 10:55:42: 31000000 INFO @ Fri, 10 Dec 2021 10:55:43: 29000000 INFO @ Fri, 10 Dec 2021 10:55:54: 32000000 INFO @ Fri, 10 Dec 2021 10:55:54: 30000000 INFO @ Fri, 10 Dec 2021 10:56:05: 31000000 INFO @ Fri, 10 Dec 2021 10:56:06: 33000000 INFO @ Fri, 10 Dec 2021 10:56:16: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 10:56:16: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 10:56:16: #1 total tags in treatment: 11344803 INFO @ Fri, 10 Dec 2021 10:56:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:56:16: #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 10:56:16: #1 tags after filtering in treatment: 6742233 INFO @ Fri, 10 Dec 2021 10:56:16: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 10 Dec 2021 10:56:16: #1 finished! INFO @ Fri, 10 Dec 2021 10:56:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:56:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:56:16: 32000000 INFO @ Fri, 10 Dec 2021 10:56:17: #2 number of paired peaks: 6829 INFO @ Fri, 10 Dec 2021 10:56:17: start model_add_line... INFO @ Fri, 10 Dec 2021 10:56:17: start X-correlation... INFO @ Fri, 10 Dec 2021 10:56:17: end of X-cor INFO @ Fri, 10 Dec 2021 10:56:17: #2 finished! INFO @ Fri, 10 Dec 2021 10:56:17: #2 predicted fragment length is 277 bps INFO @ Fri, 10 Dec 2021 10:56:17: #2 alternative fragment length(s) may be 277 bps INFO @ Fri, 10 Dec 2021 10:56:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.10_model.r WARNING @ Fri, 10 Dec 2021 10:56:17: #2 Since the d (277) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:56:17: #2 You may need to consider one of the other alternative d(s): 277 WARNING @ Fri, 10 Dec 2021 10:56:17: #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 10:56:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:56:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:56:27: 33000000 INFO @ Fri, 10 Dec 2021 10:56:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:56:36: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 10:56:36: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 10:56:36: #1 total tags in treatment: 11344803 INFO @ Fri, 10 Dec 2021 10:56:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:56:36: #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 10:56:37: #1 tags after filtering in treatment: 6742233 INFO @ Fri, 10 Dec 2021 10:56:37: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 10 Dec 2021 10:56:37: #1 finished! INFO @ Fri, 10 Dec 2021 10:56:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:56:37: #2 number of paired peaks: 6829 INFO @ Fri, 10 Dec 2021 10:56:37: start model_add_line... INFO @ Fri, 10 Dec 2021 10:56:38: start X-correlation... INFO @ Fri, 10 Dec 2021 10:56:38: end of X-cor INFO @ Fri, 10 Dec 2021 10:56:38: #2 finished! INFO @ Fri, 10 Dec 2021 10:56:38: #2 predicted fragment length is 277 bps INFO @ Fri, 10 Dec 2021 10:56:38: #2 alternative fragment length(s) may be 277 bps INFO @ Fri, 10 Dec 2021 10:56:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.20_model.r WARNING @ Fri, 10 Dec 2021 10:56:38: #2 Since the d (277) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:56:38: #2 You may need to consider one of the other alternative d(s): 277 WARNING @ Fri, 10 Dec 2021 10:56:38: #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 10:56:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:56:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:56:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:56:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:56:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.10_summits.bed INFO @ Fri, 10 Dec 2021 10:56:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6961 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:56:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:57:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:57:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:57:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412055/SRX10412055.20_summits.bed INFO @ Fri, 10 Dec 2021 10:57:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4520 records, 4 fields): 8 millis CompletedMACS2peakCalling