Job ID = 16437216 SRX = SRX12119061 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 35390528 spots for SRR15827099/SRR15827099.sra Written 35390528 spots for SRR15827099/SRR15827099.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438146 ("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: 01:18:42 35390528 reads; of these: 35390528 (100.00%) were paired; of these: 26314765 (74.36%) aligned concordantly 0 times 5967214 (16.86%) aligned concordantly exactly 1 time 3108549 (8.78%) aligned concordantly >1 times ---- 26314765 pairs aligned concordantly 0 times; of these: 2085759 (7.93%) aligned discordantly 1 time ---- 24229006 pairs aligned 0 times concordantly or discordantly; of these: 48458012 mates make up the pairs; of these: 45169289 (93.21%) aligned 0 times 1155309 (2.38%) aligned exactly 1 time 2133414 (4.40%) aligned >1 times 36.18% overall alignment rate Time searching: 01:18:42 Overall time: 01:18:42 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] 2556388 / 11089263 = 0.2305 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.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 @ Tue, 02 Aug 2022 13:58:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:58:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:58:47: 1000000 INFO @ Tue, 02 Aug 2022 13:58:58: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.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 @ Tue, 02 Aug 2022 13:59:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:59:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:59:09: 3000000 INFO @ Tue, 02 Aug 2022 13:59:16: 1000000 INFO @ Tue, 02 Aug 2022 13:59:20: 4000000 INFO @ Tue, 02 Aug 2022 13:59:27: 2000000 INFO @ Tue, 02 Aug 2022 13:59:32: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.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 @ Tue, 02 Aug 2022 13:59:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:59:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:59:38: 3000000 INFO @ Tue, 02 Aug 2022 13:59:45: 6000000 INFO @ Tue, 02 Aug 2022 13:59:46: 1000000 INFO @ Tue, 02 Aug 2022 13:59:50: 4000000 INFO @ Tue, 02 Aug 2022 13:59:57: 2000000 INFO @ Tue, 02 Aug 2022 13:59:58: 7000000 INFO @ Tue, 02 Aug 2022 14:00:02: 5000000 INFO @ Tue, 02 Aug 2022 14:00:07: 3000000 INFO @ Tue, 02 Aug 2022 14:00:10: 8000000 INFO @ Tue, 02 Aug 2022 14:00:14: 6000000 INFO @ Tue, 02 Aug 2022 14:00:18: 4000000 INFO @ Tue, 02 Aug 2022 14:00:22: 9000000 INFO @ Tue, 02 Aug 2022 14:00:26: 7000000 INFO @ Tue, 02 Aug 2022 14:00:28: 5000000 INFO @ Tue, 02 Aug 2022 14:00:37: 8000000 INFO @ Tue, 02 Aug 2022 14:00:37: 10000000 INFO @ Tue, 02 Aug 2022 14:00:39: 6000000 INFO @ Tue, 02 Aug 2022 14:00:48: 9000000 INFO @ Tue, 02 Aug 2022 14:00:49: 7000000 INFO @ Tue, 02 Aug 2022 14:00:50: 11000000 INFO @ Tue, 02 Aug 2022 14:01:00: 10000000 INFO @ Tue, 02 Aug 2022 14:01:00: 8000000 INFO @ Tue, 02 Aug 2022 14:01:02: 12000000 INFO @ Tue, 02 Aug 2022 14:01:10: 9000000 INFO @ Tue, 02 Aug 2022 14:01:11: 11000000 INFO @ Tue, 02 Aug 2022 14:01:14: 13000000 INFO @ Tue, 02 Aug 2022 14:01:21: 10000000 INFO @ Tue, 02 Aug 2022 14:01:23: 12000000 INFO @ Tue, 02 Aug 2022 14:01:25: 14000000 INFO @ Tue, 02 Aug 2022 14:01:33: 11000000 INFO @ Tue, 02 Aug 2022 14:01:34: 13000000 INFO @ Tue, 02 Aug 2022 14:01:36: 15000000 INFO @ Tue, 02 Aug 2022 14:01:46: 14000000 INFO @ Tue, 02 Aug 2022 14:01:46: 12000000 INFO @ Tue, 02 Aug 2022 14:01:46: 16000000 INFO @ Tue, 02 Aug 2022 14:01:57: 15000000 INFO @ Tue, 02 Aug 2022 14:01:58: 13000000 INFO @ Tue, 02 Aug 2022 14:01:59: 17000000 INFO @ Tue, 02 Aug 2022 14:02:07: 16000000 INFO @ Tue, 02 Aug 2022 14:02:09: 14000000 INFO @ Tue, 02 Aug 2022 14:02:11: 18000000 INFO @ Tue, 02 Aug 2022 14:02:19: 17000000 INFO @ Tue, 02 Aug 2022 14:02:19: 15000000 INFO @ Tue, 02 Aug 2022 14:02:23: 19000000 INFO @ Tue, 02 Aug 2022 14:02:29: 16000000 INFO @ Tue, 02 Aug 2022 14:02:31: 18000000 INFO @ Tue, 02 Aug 2022 14:02:35: 20000000 INFO @ Tue, 02 Aug 2022 14:02:37: 17000000 INFO @ Tue, 02 Aug 2022 14:02:40: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:02:40: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:02:40: #1 total tags in treatment: 6778592 INFO @ Tue, 02 Aug 2022 14:02:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:02:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:02:40: #1 tags after filtering in treatment: 5268200 INFO @ Tue, 02 Aug 2022 14:02:40: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 14:02:40: #1 finished! INFO @ Tue, 02 Aug 2022 14:02:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:02:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:02:41: #2 number of paired peaks: 2274 INFO @ Tue, 02 Aug 2022 14:02:41: start model_add_line... INFO @ Tue, 02 Aug 2022 14:02:41: start X-correlation... INFO @ Tue, 02 Aug 2022 14:02:41: end of X-cor INFO @ Tue, 02 Aug 2022 14:02:41: #2 finished! INFO @ Tue, 02 Aug 2022 14:02:41: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 14:02:41: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 14:02:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.05_model.r WARNING @ Tue, 02 Aug 2022 14:02:41: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:02:41: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 14:02:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:02:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:02:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:02:42: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:02:45: 18000000 INFO @ Tue, 02 Aug 2022 14:02:53: 20000000 INFO @ Tue, 02 Aug 2022 14:02:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:02:55: 19000000 INFO @ Tue, 02 Aug 2022 14:02:58: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:02:58: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:02:58: #1 total tags in treatment: 6778592 INFO @ Tue, 02 Aug 2022 14:02:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:02:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:02:58: #1 tags after filtering in treatment: 5268200 INFO @ Tue, 02 Aug 2022 14:02:58: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 14:02:58: #1 finished! INFO @ Tue, 02 Aug 2022 14:02:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:02:59: #2 number of paired peaks: 2274 INFO @ Tue, 02 Aug 2022 14:02:59: start model_add_line... INFO @ Tue, 02 Aug 2022 14:02:59: start X-correlation... INFO @ Tue, 02 Aug 2022 14:02:59: end of X-cor INFO @ Tue, 02 Aug 2022 14:02:59: #2 finished! INFO @ Tue, 02 Aug 2022 14:02:59: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 14:02:59: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 14:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.10_model.r WARNING @ Tue, 02 Aug 2022 14:02:59: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:02:59: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 14:02:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:02:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.05_summits.bed INFO @ Tue, 02 Aug 2022 14:03:01: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6954 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:03:05: 20000000 INFO @ Tue, 02 Aug 2022 14:03:10: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:03:10: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:03:10: #1 total tags in treatment: 6778592 INFO @ Tue, 02 Aug 2022 14:03:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:03:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:03:10: #1 tags after filtering in treatment: 5268200 INFO @ Tue, 02 Aug 2022 14:03:10: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 14:03:10: #1 finished! INFO @ Tue, 02 Aug 2022 14:03:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:03:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:03:10: #2 number of paired peaks: 2274 INFO @ Tue, 02 Aug 2022 14:03:10: start model_add_line... INFO @ Tue, 02 Aug 2022 14:03:10: start X-correlation... INFO @ Tue, 02 Aug 2022 14:03:10: end of X-cor INFO @ Tue, 02 Aug 2022 14:03:10: #2 finished! INFO @ Tue, 02 Aug 2022 14:03:10: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 14:03:10: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 14:03:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.20_model.r WARNING @ Tue, 02 Aug 2022 14:03:10: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:03:10: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 14:03:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:03:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:03:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:03:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:03:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:03:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.10_summits.bed INFO @ Tue, 02 Aug 2022 14:03:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3972 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:03:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:03:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:03:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:03:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119061/SRX12119061.20_summits.bed INFO @ Tue, 02 Aug 2022 14:03:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1669 records, 4 fields): 22 millis CompletedMACS2peakCalling