Job ID = 16436987 SRX = SRX12119058 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33232742 spots for SRR15827096/SRR15827096.sra Written 33232742 spots for SRR15827096/SRR15827096.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438065 ("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: 01:04:19 33232742 reads; of these: 33232742 (100.00%) were paired; of these: 22041481 (66.32%) aligned concordantly 0 times 8748987 (26.33%) aligned concordantly exactly 1 time 2442274 (7.35%) aligned concordantly >1 times ---- 22041481 pairs aligned concordantly 0 times; of these: 3190919 (14.48%) aligned discordantly 1 time ---- 18850562 pairs aligned 0 times concordantly or discordantly; of these: 37701124 mates make up the pairs; of these: 34492540 (91.49%) aligned 0 times 1609054 (4.27%) aligned exactly 1 time 1599530 (4.24%) aligned >1 times 48.10% overall alignment rate Time searching: 01:04:19 Overall time: 01:04:19 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 24 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] 2464156 / 14296343 = 0.1724 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 13:37:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.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 13:37:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:37:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:38:09: 1000000 INFO @ Tue, 02 Aug 2022 13:38:19: 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 13:38:29: 3000000 INFO @ Tue, 02 Aug 2022 13:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.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 13:38:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:38:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:38:40: 4000000 INFO @ Tue, 02 Aug 2022 13:38:41: 1000000 INFO @ Tue, 02 Aug 2022 13:38:51: 5000000 INFO @ Tue, 02 Aug 2022 13:38:53: 2000000 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 13:38:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.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 13:38:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:38:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:39:03: 6000000 INFO @ Tue, 02 Aug 2022 13:39:05: 3000000 INFO @ Tue, 02 Aug 2022 13:39:11: 1000000 INFO @ Tue, 02 Aug 2022 13:39:15: 7000000 INFO @ Tue, 02 Aug 2022 13:39:16: 4000000 INFO @ Tue, 02 Aug 2022 13:39:22: 2000000 INFO @ Tue, 02 Aug 2022 13:39:27: 8000000 INFO @ Tue, 02 Aug 2022 13:39:28: 5000000 INFO @ Tue, 02 Aug 2022 13:39:34: 3000000 INFO @ Tue, 02 Aug 2022 13:39:39: 6000000 INFO @ Tue, 02 Aug 2022 13:39:40: 9000000 INFO @ Tue, 02 Aug 2022 13:39:46: 4000000 INFO @ Tue, 02 Aug 2022 13:39:51: 7000000 INFO @ Tue, 02 Aug 2022 13:39:52: 10000000 INFO @ Tue, 02 Aug 2022 13:39:57: 5000000 INFO @ Tue, 02 Aug 2022 13:40:02: 8000000 INFO @ Tue, 02 Aug 2022 13:40:04: 11000000 INFO @ Tue, 02 Aug 2022 13:40:09: 6000000 INFO @ Tue, 02 Aug 2022 13:40:13: 9000000 INFO @ Tue, 02 Aug 2022 13:40:17: 12000000 INFO @ Tue, 02 Aug 2022 13:40:20: 7000000 INFO @ Tue, 02 Aug 2022 13:40:25: 10000000 INFO @ Tue, 02 Aug 2022 13:40:29: 13000000 INFO @ Tue, 02 Aug 2022 13:40:32: 8000000 INFO @ Tue, 02 Aug 2022 13:40:36: 11000000 INFO @ Tue, 02 Aug 2022 13:40:42: 14000000 INFO @ Tue, 02 Aug 2022 13:40:45: 9000000 INFO @ Tue, 02 Aug 2022 13:40:46: 12000000 INFO @ Tue, 02 Aug 2022 13:40:54: 15000000 INFO @ Tue, 02 Aug 2022 13:40:56: 10000000 INFO @ Tue, 02 Aug 2022 13:40:57: 13000000 INFO @ Tue, 02 Aug 2022 13:41:07: 16000000 INFO @ Tue, 02 Aug 2022 13:41:08: 14000000 INFO @ Tue, 02 Aug 2022 13:41:09: 11000000 INFO @ Tue, 02 Aug 2022 13:41:19: 15000000 INFO @ Tue, 02 Aug 2022 13:41:20: 17000000 INFO @ Tue, 02 Aug 2022 13:41:21: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:41:30: 16000000 INFO @ Tue, 02 Aug 2022 13:41:32: 18000000 INFO @ Tue, 02 Aug 2022 13:41:34: 13000000 INFO @ Tue, 02 Aug 2022 13:41:40: 17000000 INFO @ Tue, 02 Aug 2022 13:41:44: 19000000 INFO @ Tue, 02 Aug 2022 13:41:46: 14000000 INFO @ Tue, 02 Aug 2022 13:41:51: 18000000 INFO @ Tue, 02 Aug 2022 13:41:57: 20000000 INFO @ Tue, 02 Aug 2022 13:41:58: 15000000 INFO @ Tue, 02 Aug 2022 13:42:02: 19000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:42:09: 21000000 INFO @ Tue, 02 Aug 2022 13:42:11: 16000000 INFO @ Tue, 02 Aug 2022 13:42:12: 20000000 INFO @ Tue, 02 Aug 2022 13:42:21: 22000000 INFO @ Tue, 02 Aug 2022 13:42:23: 21000000 INFO @ Tue, 02 Aug 2022 13:42:23: 17000000 INFO @ Tue, 02 Aug 2022 13:42:33: 23000000 INFO @ Tue, 02 Aug 2022 13:42:34: 22000000 INFO @ Tue, 02 Aug 2022 13:42:35: 18000000 INFO @ Tue, 02 Aug 2022 13:42:46: 23000000 INFO @ Tue, 02 Aug 2022 13:42:46: 24000000 INFO @ Tue, 02 Aug 2022 13:42:48: 19000000 INFO @ Tue, 02 Aug 2022 13:42:57: 24000000 INFO @ Tue, 02 Aug 2022 13:42:59: 25000000 INFO @ Tue, 02 Aug 2022 13:43:00: 20000000 INFO @ Tue, 02 Aug 2022 13:43:08: 25000000 INFO @ Tue, 02 Aug 2022 13:43:11: 26000000 INFO @ Tue, 02 Aug 2022 13:43:12: 21000000 INFO @ Tue, 02 Aug 2022 13:43:18: 26000000 INFO @ Tue, 02 Aug 2022 13:43:23: 27000000 INFO @ Tue, 02 Aug 2022 13:43:23: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:43:23: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:43:23: #1 total tags in treatment: 9149438 INFO @ Tue, 02 Aug 2022 13:43:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:43:23: #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 13:43:23: #1 tags after filtering in treatment: 6951862 INFO @ Tue, 02 Aug 2022 13:43:23: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 13:43:23: #1 finished! INFO @ Tue, 02 Aug 2022 13:43:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:43:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:43:24: #2 number of paired peaks: 1909 INFO @ Tue, 02 Aug 2022 13:43:24: start model_add_line... INFO @ Tue, 02 Aug 2022 13:43:24: start X-correlation... INFO @ Tue, 02 Aug 2022 13:43:24: end of X-cor INFO @ Tue, 02 Aug 2022 13:43:24: #2 finished! INFO @ Tue, 02 Aug 2022 13:43:24: #2 predicted fragment length is 218 bps INFO @ Tue, 02 Aug 2022 13:43:24: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 02 Aug 2022 13:43:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.05_model.r INFO @ Tue, 02 Aug 2022 13:43:24: 22000000 WARNING @ Tue, 02 Aug 2022 13:43:24: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:43:24: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Tue, 02 Aug 2022 13:43:24: #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 13:43:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:43:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:43:29: 27000000 INFO @ Tue, 02 Aug 2022 13:43:30: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:43:30: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:43:30: #1 total tags in treatment: 9149438 INFO @ Tue, 02 Aug 2022 13:43:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:43:30: #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 13:43:30: #1 tags after filtering in treatment: 6951862 INFO @ Tue, 02 Aug 2022 13:43:30: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 13:43:30: #1 finished! INFO @ Tue, 02 Aug 2022 13:43:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:43:30: #2 number of paired peaks: 1909 INFO @ Tue, 02 Aug 2022 13:43:30: start model_add_line... INFO @ Tue, 02 Aug 2022 13:43:30: start X-correlation... INFO @ Tue, 02 Aug 2022 13:43:30: end of X-cor INFO @ Tue, 02 Aug 2022 13:43:30: #2 finished! INFO @ Tue, 02 Aug 2022 13:43:30: #2 predicted fragment length is 218 bps INFO @ Tue, 02 Aug 2022 13:43:30: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 02 Aug 2022 13:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.10_model.r WARNING @ Tue, 02 Aug 2022 13:43:30: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:43:30: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Tue, 02 Aug 2022 13:43:30: #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 13:43:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:43:35: 23000000 INFO @ Tue, 02 Aug 2022 13:43:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:43:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:43:47: 24000000 INFO @ Tue, 02 Aug 2022 13:43:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:43:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:43:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.05_summits.bed INFO @ Tue, 02 Aug 2022 13:43:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8085 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:43:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:43:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:43:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.10_summits.bed INFO @ Tue, 02 Aug 2022 13:43:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4951 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:43:56: 25000000 INFO @ Tue, 02 Aug 2022 13:44:06: 26000000 INFO @ Tue, 02 Aug 2022 13:44:16: 27000000 INFO @ Tue, 02 Aug 2022 13:44:16: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:44:16: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:44:16: #1 total tags in treatment: 9149438 INFO @ Tue, 02 Aug 2022 13:44:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:44:16: #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 13:44:16: #1 tags after filtering in treatment: 6951862 INFO @ Tue, 02 Aug 2022 13:44:16: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 13:44:16: #1 finished! INFO @ Tue, 02 Aug 2022 13:44:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:44:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:44:17: #2 number of paired peaks: 1909 INFO @ Tue, 02 Aug 2022 13:44:17: start model_add_line... INFO @ Tue, 02 Aug 2022 13:44:17: start X-correlation... INFO @ Tue, 02 Aug 2022 13:44:17: end of X-cor INFO @ Tue, 02 Aug 2022 13:44:17: #2 finished! INFO @ Tue, 02 Aug 2022 13:44:17: #2 predicted fragment length is 218 bps INFO @ Tue, 02 Aug 2022 13:44:17: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 02 Aug 2022 13:44:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.20_model.r WARNING @ Tue, 02 Aug 2022 13:44:17: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:44:17: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Tue, 02 Aug 2022 13:44:17: #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 13:44:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:44:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:44:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:44:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:44:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:44:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119058/SRX12119058.20_summits.bed INFO @ Tue, 02 Aug 2022 13:44:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2157 records, 4 fields): 83 millis CompletedMACS2peakCalling