Job ID = 14171976 SRX = SRX7889136 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23091984 spots for SRR11283126/SRR11283126.sra Written 23091984 spots for SRR11283126/SRR11283126.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172559 ("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: 00:41:15 23091984 reads; of these: 23091984 (100.00%) were paired; of these: 8380928 (36.29%) aligned concordantly 0 times 13017021 (56.37%) aligned concordantly exactly 1 time 1694035 (7.34%) aligned concordantly >1 times ---- 8380928 pairs aligned concordantly 0 times; of these: 1940295 (23.15%) aligned discordantly 1 time ---- 6440633 pairs aligned 0 times concordantly or discordantly; of these: 12881266 mates make up the pairs; of these: 10518309 (81.66%) aligned 0 times 1731688 (13.44%) aligned exactly 1 time 631269 (4.90%) aligned >1 times 77.23% overall alignment rate Time searching: 00:41:15 Overall time: 00:41:16 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 28 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] 1685946 / 15745527 = 0.1071 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 14:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.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 14:40:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:40:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:41:04: 1000000 INFO @ Sat, 11 Dec 2021 14:41:13: 2000000 INFO @ Sat, 11 Dec 2021 14:41:21: 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 14:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.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 14:41:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:41:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:41:30: 4000000 INFO @ Sat, 11 Dec 2021 14:41:35: 1000000 INFO @ Sat, 11 Dec 2021 14:41:39: 5000000 INFO @ Sat, 11 Dec 2021 14:41:44: 2000000 INFO @ Sat, 11 Dec 2021 14:41:48: 6000000 INFO @ Sat, 11 Dec 2021 14:41:52: 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 14:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.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 14:41:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:41:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:41:57: 7000000 INFO @ Sat, 11 Dec 2021 14:42:01: 4000000 INFO @ Sat, 11 Dec 2021 14:42:05: 1000000 INFO @ Sat, 11 Dec 2021 14:42:06: 8000000 INFO @ Sat, 11 Dec 2021 14:42:10: 5000000 INFO @ Sat, 11 Dec 2021 14:42:15: 2000000 INFO @ Sat, 11 Dec 2021 14:42:15: 9000000 INFO @ Sat, 11 Dec 2021 14:42:19: 6000000 INFO @ Sat, 11 Dec 2021 14:42:24: 3000000 INFO @ Sat, 11 Dec 2021 14:42:24: 10000000 INFO @ Sat, 11 Dec 2021 14:42:28: 7000000 INFO @ Sat, 11 Dec 2021 14:42:33: 11000000 INFO @ Sat, 11 Dec 2021 14:42:33: 4000000 INFO @ Sat, 11 Dec 2021 14:42:37: 8000000 INFO @ Sat, 11 Dec 2021 14:42:42: 12000000 INFO @ Sat, 11 Dec 2021 14:42:43: 5000000 INFO @ Sat, 11 Dec 2021 14:42:46: 9000000 INFO @ Sat, 11 Dec 2021 14:42:51: 13000000 INFO @ Sat, 11 Dec 2021 14:42:52: 6000000 INFO @ Sat, 11 Dec 2021 14:42:55: 10000000 INFO @ Sat, 11 Dec 2021 14:43:00: 14000000 INFO @ Sat, 11 Dec 2021 14:43:01: 7000000 INFO @ Sat, 11 Dec 2021 14:43:04: 11000000 INFO @ Sat, 11 Dec 2021 14:43:09: 15000000 INFO @ Sat, 11 Dec 2021 14:43:10: 8000000 INFO @ Sat, 11 Dec 2021 14:43:13: 12000000 INFO @ Sat, 11 Dec 2021 14:43:18: 16000000 INFO @ Sat, 11 Dec 2021 14:43:20: 9000000 INFO @ Sat, 11 Dec 2021 14:43:22: 13000000 INFO @ Sat, 11 Dec 2021 14:43:27: 17000000 INFO @ Sat, 11 Dec 2021 14:43:29: 10000000 INFO @ Sat, 11 Dec 2021 14:43:31: 14000000 INFO @ Sat, 11 Dec 2021 14:43:36: 18000000 INFO @ Sat, 11 Dec 2021 14:43:38: 11000000 INFO @ Sat, 11 Dec 2021 14:43:40: 15000000 INFO @ Sat, 11 Dec 2021 14:43:44: 19000000 INFO @ Sat, 11 Dec 2021 14:43:47: 12000000 INFO @ Sat, 11 Dec 2021 14:43:48: 16000000 INFO @ Sat, 11 Dec 2021 14:43:53: 20000000 INFO @ Sat, 11 Dec 2021 14:43:57: 13000000 INFO @ Sat, 11 Dec 2021 14:43:57: 17000000 INFO @ Sat, 11 Dec 2021 14:44:02: 21000000 INFO @ Sat, 11 Dec 2021 14:44:06: 14000000 INFO @ Sat, 11 Dec 2021 14:44:06: 18000000 INFO @ Sat, 11 Dec 2021 14:44:11: 22000000 INFO @ Sat, 11 Dec 2021 14:44:15: 15000000 INFO @ Sat, 11 Dec 2021 14:44:15: 19000000 INFO @ Sat, 11 Dec 2021 14:44:20: 23000000 INFO @ Sat, 11 Dec 2021 14:44:24: 20000000 INFO @ Sat, 11 Dec 2021 14:44:24: 16000000 INFO @ Sat, 11 Dec 2021 14:44:29: 24000000 INFO @ Sat, 11 Dec 2021 14:44:33: 21000000 INFO @ Sat, 11 Dec 2021 14:44:33: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:44:38: 25000000 INFO @ Sat, 11 Dec 2021 14:44:42: 22000000 INFO @ Sat, 11 Dec 2021 14:44:43: 18000000 INFO @ Sat, 11 Dec 2021 14:44:47: 26000000 INFO @ Sat, 11 Dec 2021 14:44:51: 23000000 INFO @ Sat, 11 Dec 2021 14:44:52: 19000000 INFO @ Sat, 11 Dec 2021 14:44:56: 27000000 INFO @ Sat, 11 Dec 2021 14:44:59: 24000000 INFO @ Sat, 11 Dec 2021 14:45:01: 20000000 INFO @ Sat, 11 Dec 2021 14:45:05: 28000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:45:08: 25000000 INFO @ Sat, 11 Dec 2021 14:45:10: 21000000 INFO @ Sat, 11 Dec 2021 14:45:14: 29000000 INFO @ Sat, 11 Dec 2021 14:45:17: 26000000 INFO @ Sat, 11 Dec 2021 14:45:20: 22000000 INFO @ Sat, 11 Dec 2021 14:45:23: 30000000 INFO @ Sat, 11 Dec 2021 14:45:26: 27000000 INFO @ Sat, 11 Dec 2021 14:45:29: 23000000 INFO @ Sat, 11 Dec 2021 14:45:32: 31000000 INFO @ Sat, 11 Dec 2021 14:45:35: 28000000 INFO @ Sat, 11 Dec 2021 14:45:38: 24000000 INFO @ Sat, 11 Dec 2021 14:45:41: 32000000 INFO @ Sat, 11 Dec 2021 14:45:44: #1 tag size is determined as 144 bps INFO @ Sat, 11 Dec 2021 14:45:44: #1 tag size = 144 INFO @ Sat, 11 Dec 2021 14:45:44: #1 total tags in treatment: 13164711 INFO @ Sat, 11 Dec 2021 14:45:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:45:44: #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 14:45:44: #1 tags after filtering in treatment: 8082011 INFO @ Sat, 11 Dec 2021 14:45:44: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 11 Dec 2021 14:45:44: #1 finished! INFO @ Sat, 11 Dec 2021 14:45:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:45:44: 29000000 INFO @ Sat, 11 Dec 2021 14:45:45: #2 number of paired peaks: 6780 INFO @ Sat, 11 Dec 2021 14:45:45: start model_add_line... INFO @ Sat, 11 Dec 2021 14:45:45: start X-correlation... INFO @ Sat, 11 Dec 2021 14:45:45: end of X-cor INFO @ Sat, 11 Dec 2021 14:45:45: #2 finished! INFO @ Sat, 11 Dec 2021 14:45:45: #2 predicted fragment length is 280 bps INFO @ Sat, 11 Dec 2021 14:45:45: #2 alternative fragment length(s) may be 280 bps INFO @ Sat, 11 Dec 2021 14:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.05_model.r WARNING @ Sat, 11 Dec 2021 14:45:45: #2 Since the d (280) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:45:45: #2 You may need to consider one of the other alternative d(s): 280 WARNING @ Sat, 11 Dec 2021 14:45:45: #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 14:45:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:45:48: 25000000 INFO @ Sat, 11 Dec 2021 14:45:53: 30000000 INFO @ Sat, 11 Dec 2021 14:45:57: 26000000 INFO @ Sat, 11 Dec 2021 14:46:02: 31000000 INFO @ Sat, 11 Dec 2021 14:46:06: 27000000 INFO @ Sat, 11 Dec 2021 14:46:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:46:10: 32000000 INFO @ Sat, 11 Dec 2021 14:46:13: #1 tag size is determined as 144 bps INFO @ Sat, 11 Dec 2021 14:46:13: #1 tag size = 144 INFO @ Sat, 11 Dec 2021 14:46:13: #1 total tags in treatment: 13164711 INFO @ Sat, 11 Dec 2021 14:46:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:46:13: #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 14:46:13: #1 tags after filtering in treatment: 8082011 INFO @ Sat, 11 Dec 2021 14:46:13: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 11 Dec 2021 14:46:13: #1 finished! INFO @ Sat, 11 Dec 2021 14:46:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:46:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:46:14: #2 number of paired peaks: 6780 INFO @ Sat, 11 Dec 2021 14:46:14: start model_add_line... INFO @ Sat, 11 Dec 2021 14:46:15: start X-correlation... INFO @ Sat, 11 Dec 2021 14:46:15: end of X-cor INFO @ Sat, 11 Dec 2021 14:46:15: #2 finished! INFO @ Sat, 11 Dec 2021 14:46:15: #2 predicted fragment length is 280 bps INFO @ Sat, 11 Dec 2021 14:46:15: #2 alternative fragment length(s) may be 280 bps INFO @ Sat, 11 Dec 2021 14:46:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.10_model.r WARNING @ Sat, 11 Dec 2021 14:46:15: #2 Since the d (280) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:46:15: #2 You may need to consider one of the other alternative d(s): 280 WARNING @ Sat, 11 Dec 2021 14:46:15: #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 14:46:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:46:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:46:16: 28000000 INFO @ Sat, 11 Dec 2021 14:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.05_summits.bed INFO @ Sat, 11 Dec 2021 14:46:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7387 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:46:24: 29000000 INFO @ Sat, 11 Dec 2021 14:46:33: 30000000 INFO @ Sat, 11 Dec 2021 14:46:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:46:42: 31000000 INFO @ Sat, 11 Dec 2021 14:46:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:46:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:46:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.10_summits.bed INFO @ Sat, 11 Dec 2021 14:46:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6473 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:46:51: 32000000 INFO @ Sat, 11 Dec 2021 14:46:54: #1 tag size is determined as 144 bps INFO @ Sat, 11 Dec 2021 14:46:54: #1 tag size = 144 INFO @ Sat, 11 Dec 2021 14:46:54: #1 total tags in treatment: 13164711 INFO @ Sat, 11 Dec 2021 14:46:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:46:54: #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 14:46:54: #1 tags after filtering in treatment: 8082011 INFO @ Sat, 11 Dec 2021 14:46:54: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 11 Dec 2021 14:46:54: #1 finished! INFO @ Sat, 11 Dec 2021 14:46:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:46:55: #2 number of paired peaks: 6780 INFO @ Sat, 11 Dec 2021 14:46:55: start model_add_line... INFO @ Sat, 11 Dec 2021 14:46:55: start X-correlation... INFO @ Sat, 11 Dec 2021 14:46:55: end of X-cor INFO @ Sat, 11 Dec 2021 14:46:55: #2 finished! INFO @ Sat, 11 Dec 2021 14:46:55: #2 predicted fragment length is 280 bps INFO @ Sat, 11 Dec 2021 14:46:55: #2 alternative fragment length(s) may be 280 bps INFO @ Sat, 11 Dec 2021 14:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.20_model.r WARNING @ Sat, 11 Dec 2021 14:46:55: #2 Since the d (280) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:46:55: #2 You may need to consider one of the other alternative d(s): 280 WARNING @ Sat, 11 Dec 2021 14:46:55: #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 14:46:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:46:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:47:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889136/SRX7889136.20_summits.bed INFO @ Sat, 11 Dec 2021 14:47:27: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5754 records, 4 fields): 7 millis CompletedMACS2peakCalling