Job ID = 14170624 SRX = SRX9660890 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25131269 spots for SRR13228530/SRR13228530.sra Written 25131269 spots for SRR13228530/SRR13228530.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171263 ("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: 01:07:21 25131269 reads; of these: 25131269 (100.00%) were paired; of these: 8092207 (32.20%) aligned concordantly 0 times 15038129 (59.84%) aligned concordantly exactly 1 time 2000933 (7.96%) aligned concordantly >1 times ---- 8092207 pairs aligned concordantly 0 times; of these: 1945741 (24.04%) aligned discordantly 1 time ---- 6146466 pairs aligned 0 times concordantly or discordantly; of these: 12292932 mates make up the pairs; of these: 10692617 (86.98%) aligned 0 times 953070 (7.75%) aligned exactly 1 time 647245 (5.27%) aligned >1 times 78.73% overall alignment rate Time searching: 01:07:21 Overall time: 01:07:21 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] 3062941 / 17662268 = 0.1734 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 09:11:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.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 09:11:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:11:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:11:55: 1000000 INFO @ Sat, 11 Dec 2021 09:12:07: 2000000 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 09:12:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.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 09:12:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:12:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:12:19: 3000000 INFO @ Sat, 11 Dec 2021 09:12:26: 1000000 INFO @ Sat, 11 Dec 2021 09:12:31: 4000000 INFO @ Sat, 11 Dec 2021 09:12:38: 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 @ Sat, 11 Dec 2021 09:12:43: 5000000 INFO @ Sat, 11 Dec 2021 09:12:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.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 09:12:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:12:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:12:51: 3000000 INFO @ Sat, 11 Dec 2021 09:12:56: 6000000 INFO @ Sat, 11 Dec 2021 09:12:56: 1000000 INFO @ Sat, 11 Dec 2021 09:13:03: 4000000 INFO @ Sat, 11 Dec 2021 09:13:08: 7000000 INFO @ Sat, 11 Dec 2021 09:13:09: 2000000 INFO @ Sat, 11 Dec 2021 09:13:16: 5000000 INFO @ Sat, 11 Dec 2021 09:13:21: 8000000 INFO @ Sat, 11 Dec 2021 09:13:21: 3000000 INFO @ Sat, 11 Dec 2021 09:13:28: 6000000 INFO @ Sat, 11 Dec 2021 09:13:33: 4000000 INFO @ Sat, 11 Dec 2021 09:13:33: 9000000 INFO @ Sat, 11 Dec 2021 09:13:40: 7000000 INFO @ Sat, 11 Dec 2021 09:13:45: 10000000 INFO @ Sat, 11 Dec 2021 09:13:46: 5000000 INFO @ Sat, 11 Dec 2021 09:13:53: 8000000 INFO @ Sat, 11 Dec 2021 09:13:58: 11000000 INFO @ Sat, 11 Dec 2021 09:13:59: 6000000 INFO @ Sat, 11 Dec 2021 09:14:05: 9000000 INFO @ Sat, 11 Dec 2021 09:14:10: 12000000 INFO @ Sat, 11 Dec 2021 09:14:12: 7000000 INFO @ Sat, 11 Dec 2021 09:14:18: 10000000 INFO @ Sat, 11 Dec 2021 09:14:22: 13000000 INFO @ Sat, 11 Dec 2021 09:14:25: 8000000 INFO @ Sat, 11 Dec 2021 09:14:30: 11000000 INFO @ Sat, 11 Dec 2021 09:14:36: 14000000 INFO @ Sat, 11 Dec 2021 09:14:37: 9000000 INFO @ Sat, 11 Dec 2021 09:14:43: 12000000 INFO @ Sat, 11 Dec 2021 09:14:49: 15000000 INFO @ Sat, 11 Dec 2021 09:14:50: 10000000 INFO @ Sat, 11 Dec 2021 09:14:55: 13000000 INFO @ Sat, 11 Dec 2021 09:15:02: 11000000 INFO @ Sat, 11 Dec 2021 09:15:03: 16000000 INFO @ Sat, 11 Dec 2021 09:15:08: 14000000 INFO @ Sat, 11 Dec 2021 09:15:15: 12000000 INFO @ Sat, 11 Dec 2021 09:15:16: 17000000 INFO @ Sat, 11 Dec 2021 09:15:21: 15000000 INFO @ Sat, 11 Dec 2021 09:15:27: 13000000 INFO @ Sat, 11 Dec 2021 09:15:28: 18000000 INFO @ Sat, 11 Dec 2021 09:15:33: 16000000 INFO @ Sat, 11 Dec 2021 09:15:40: 19000000 INFO @ Sat, 11 Dec 2021 09:15:41: 14000000 INFO @ Sat, 11 Dec 2021 09:15:46: 17000000 INFO @ Sat, 11 Dec 2021 09:15:52: 20000000 INFO @ Sat, 11 Dec 2021 09:15:54: 15000000 INFO @ Sat, 11 Dec 2021 09:15:58: 18000000 INFO @ Sat, 11 Dec 2021 09:16:04: 21000000 INFO @ Sat, 11 Dec 2021 09:16:08: 16000000 INFO @ Sat, 11 Dec 2021 09:16:11: 19000000 INFO @ Sat, 11 Dec 2021 09:16:16: 22000000 INFO @ Sat, 11 Dec 2021 09:16:21: 17000000 INFO @ Sat, 11 Dec 2021 09:16:23: 20000000 INFO @ Sat, 11 Dec 2021 09:16:29: 23000000 INFO @ Sat, 11 Dec 2021 09:16:33: 18000000 INFO @ Sat, 11 Dec 2021 09:16:35: 21000000 INFO @ Sat, 11 Dec 2021 09:16:41: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:16:46: 19000000 INFO @ Sat, 11 Dec 2021 09:16:48: 22000000 INFO @ Sat, 11 Dec 2021 09:16:53: 25000000 INFO @ Sat, 11 Dec 2021 09:16:59: 20000000 INFO @ Sat, 11 Dec 2021 09:17:00: 23000000 INFO @ Sat, 11 Dec 2021 09:17:06: 26000000 INFO @ Sat, 11 Dec 2021 09:17:12: 21000000 INFO @ Sat, 11 Dec 2021 09:17:13: 24000000 INFO @ Sat, 11 Dec 2021 09:17:18: 27000000 INFO @ Sat, 11 Dec 2021 09:17:25: 22000000 INFO @ Sat, 11 Dec 2021 09:17:25: 25000000 INFO @ Sat, 11 Dec 2021 09:17:31: 28000000 INFO @ Sat, 11 Dec 2021 09:17:38: 26000000 INFO @ Sat, 11 Dec 2021 09:17:38: 23000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:17:44: 29000000 INFO @ Sat, 11 Dec 2021 09:17:50: 27000000 INFO @ Sat, 11 Dec 2021 09:17:51: 24000000 INFO @ Sat, 11 Dec 2021 09:17:56: 30000000 INFO @ Sat, 11 Dec 2021 09:18:03: 28000000 INFO @ Sat, 11 Dec 2021 09:18:03: 25000000 INFO @ Sat, 11 Dec 2021 09:18:09: 31000000 INFO @ Sat, 11 Dec 2021 09:18:16: 29000000 INFO @ Sat, 11 Dec 2021 09:18:16: 26000000 INFO @ Sat, 11 Dec 2021 09:18:21: 32000000 INFO @ Sat, 11 Dec 2021 09:18:28: 30000000 INFO @ Sat, 11 Dec 2021 09:18:29: 27000000 INFO @ Sat, 11 Dec 2021 09:18:32: 33000000 INFO @ Sat, 11 Dec 2021 09:18:38: #1 tag size is determined as 140 bps INFO @ Sat, 11 Dec 2021 09:18:38: #1 tag size = 140 INFO @ Sat, 11 Dec 2021 09:18:38: #1 total tags in treatment: 14191060 INFO @ Sat, 11 Dec 2021 09:18:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:18:38: #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 09:18:38: #1 tags after filtering in treatment: 9635900 INFO @ Sat, 11 Dec 2021 09:18:38: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 11 Dec 2021 09:18:38: #1 finished! INFO @ Sat, 11 Dec 2021 09:18:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:18:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:18:39: #2 number of paired peaks: 2681 INFO @ Sat, 11 Dec 2021 09:18:39: start model_add_line... INFO @ Sat, 11 Dec 2021 09:18:39: start X-correlation... INFO @ Sat, 11 Dec 2021 09:18:39: end of X-cor INFO @ Sat, 11 Dec 2021 09:18:39: #2 finished! INFO @ Sat, 11 Dec 2021 09:18:39: #2 predicted fragment length is 269 bps INFO @ Sat, 11 Dec 2021 09:18:39: #2 alternative fragment length(s) may be 269 bps INFO @ Sat, 11 Dec 2021 09:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.05_model.r WARNING @ Sat, 11 Dec 2021 09:18:39: #2 Since the d (269) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:18:39: #2 You may need to consider one of the other alternative d(s): 269 WARNING @ Sat, 11 Dec 2021 09:18:39: #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 09:18:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:18:41: 31000000 INFO @ Sat, 11 Dec 2021 09:18:42: 28000000 INFO @ Sat, 11 Dec 2021 09:18:53: 32000000 INFO @ Sat, 11 Dec 2021 09:18:54: 29000000 INFO @ Sat, 11 Dec 2021 09:19:05: 33000000 INFO @ Sat, 11 Dec 2021 09:19:07: 30000000 INFO @ Sat, 11 Dec 2021 09:19:10: #1 tag size is determined as 140 bps INFO @ Sat, 11 Dec 2021 09:19:10: #1 tag size = 140 INFO @ Sat, 11 Dec 2021 09:19:10: #1 total tags in treatment: 14191060 INFO @ Sat, 11 Dec 2021 09:19:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:19:10: #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 09:19:10: #1 tags after filtering in treatment: 9635900 INFO @ Sat, 11 Dec 2021 09:19:10: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 11 Dec 2021 09:19:10: #1 finished! INFO @ Sat, 11 Dec 2021 09:19:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:19:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:19:11: #2 number of paired peaks: 2681 INFO @ Sat, 11 Dec 2021 09:19:11: start model_add_line... INFO @ Sat, 11 Dec 2021 09:19:12: start X-correlation... INFO @ Sat, 11 Dec 2021 09:19:12: end of X-cor INFO @ Sat, 11 Dec 2021 09:19:12: #2 finished! INFO @ Sat, 11 Dec 2021 09:19:12: #2 predicted fragment length is 269 bps INFO @ Sat, 11 Dec 2021 09:19:12: #2 alternative fragment length(s) may be 269 bps INFO @ Sat, 11 Dec 2021 09:19:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.10_model.r WARNING @ Sat, 11 Dec 2021 09:19:12: #2 Since the d (269) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:19:12: #2 You may need to consider one of the other alternative d(s): 269 WARNING @ Sat, 11 Dec 2021 09:19:12: #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 09:19:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:19:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:19:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:19:19: 31000000 INFO @ Sat, 11 Dec 2021 09:19:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.05_summits.bed INFO @ Sat, 11 Dec 2021 09:19:29: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7169 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:19:31: 32000000 INFO @ Sat, 11 Dec 2021 09:19:43: 33000000 INFO @ Sat, 11 Dec 2021 09:19:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:19:49: #1 tag size is determined as 140 bps INFO @ Sat, 11 Dec 2021 09:19:49: #1 tag size = 140 INFO @ Sat, 11 Dec 2021 09:19:49: #1 total tags in treatment: 14191060 INFO @ Sat, 11 Dec 2021 09:19:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:19:49: #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 09:19:49: #1 tags after filtering in treatment: 9635900 INFO @ Sat, 11 Dec 2021 09:19:49: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 11 Dec 2021 09:19:49: #1 finished! INFO @ Sat, 11 Dec 2021 09:19:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:19:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:19:50: #2 number of paired peaks: 2681 INFO @ Sat, 11 Dec 2021 09:19:50: start model_add_line... INFO @ Sat, 11 Dec 2021 09:19:50: start X-correlation... INFO @ Sat, 11 Dec 2021 09:19:50: end of X-cor INFO @ Sat, 11 Dec 2021 09:19:50: #2 finished! INFO @ Sat, 11 Dec 2021 09:19:50: #2 predicted fragment length is 269 bps INFO @ Sat, 11 Dec 2021 09:19:50: #2 alternative fragment length(s) may be 269 bps INFO @ Sat, 11 Dec 2021 09:19:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.20_model.r WARNING @ Sat, 11 Dec 2021 09:19:50: #2 Since the d (269) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:19:50: #2 You may need to consider one of the other alternative d(s): 269 WARNING @ Sat, 11 Dec 2021 09:19:50: #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 09:19:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:20:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:20:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:20:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.10_summits.bed INFO @ Sat, 11 Dec 2021 09:20:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5319 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:20:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:20:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:20:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:20:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9660890/SRX9660890.20_summits.bed INFO @ Sat, 11 Dec 2021 09:20:40: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3491 records, 4 fields): 9 millis CompletedMACS2peakCalling