Job ID = 16440037 SRX = SRX10855764 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12355045 spots for SRR14509951/SRR14509951.sra Written 12355045 spots for SRR14509951/SRR14509951.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440137 ("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: 00:30:28 12355045 reads; of these: 12355045 (100.00%) were paired; of these: 1316809 (10.66%) aligned concordantly 0 times 7844295 (63.49%) aligned concordantly exactly 1 time 3193941 (25.85%) aligned concordantly >1 times ---- 1316809 pairs aligned concordantly 0 times; of these: 236125 (17.93%) aligned discordantly 1 time ---- 1080684 pairs aligned 0 times concordantly or discordantly; of these: 2161368 mates make up the pairs; of these: 1785329 (82.60%) aligned 0 times 222423 (10.29%) aligned exactly 1 time 153616 (7.11%) aligned >1 times 92.77% overall alignment rate Time searching: 00:30:28 Overall time: 00:30:28 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 12 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] 1816083 / 11238163 = 0.1616 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 17:23:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.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 17:23:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:23:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:23:37: 1000000 INFO @ Tue, 02 Aug 2022 17:23:43: 2000000 INFO @ Tue, 02 Aug 2022 17:23:50: 3000000 INFO @ Tue, 02 Aug 2022 17:23:57: 4000000 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 17:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.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 17:23:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:23:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:24:04: 5000000 INFO @ Tue, 02 Aug 2022 17:24:08: 1000000 INFO @ Tue, 02 Aug 2022 17:24:12: 6000000 INFO @ Tue, 02 Aug 2022 17:24:16: 2000000 INFO @ Tue, 02 Aug 2022 17:24:20: 7000000 INFO @ Tue, 02 Aug 2022 17:24:23: 3000000 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 17:24:28: 8000000 INFO @ Tue, 02 Aug 2022 17:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.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 17:24:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:24:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:24:31: 4000000 INFO @ Tue, 02 Aug 2022 17:24:36: 9000000 INFO @ Tue, 02 Aug 2022 17:24:37: 1000000 INFO @ Tue, 02 Aug 2022 17:24:39: 5000000 INFO @ Tue, 02 Aug 2022 17:24:44: 10000000 INFO @ Tue, 02 Aug 2022 17:24:45: 2000000 INFO @ Tue, 02 Aug 2022 17:24:47: 6000000 INFO @ Tue, 02 Aug 2022 17:24:52: 11000000 INFO @ Tue, 02 Aug 2022 17:24:53: 3000000 INFO @ Tue, 02 Aug 2022 17:24:55: 7000000 INFO @ Tue, 02 Aug 2022 17:25:00: 12000000 INFO @ Tue, 02 Aug 2022 17:25:01: 4000000 INFO @ Tue, 02 Aug 2022 17:25:03: 8000000 INFO @ Tue, 02 Aug 2022 17:25:08: 13000000 INFO @ Tue, 02 Aug 2022 17:25:09: 5000000 INFO @ Tue, 02 Aug 2022 17:25:11: 9000000 INFO @ Tue, 02 Aug 2022 17:25:16: 14000000 INFO @ Tue, 02 Aug 2022 17:25:17: 6000000 INFO @ Tue, 02 Aug 2022 17:25:19: 10000000 INFO @ Tue, 02 Aug 2022 17:25:24: 15000000 INFO @ Tue, 02 Aug 2022 17:25:25: 7000000 INFO @ Tue, 02 Aug 2022 17:25:27: 11000000 INFO @ Tue, 02 Aug 2022 17:25:32: 16000000 INFO @ Tue, 02 Aug 2022 17:25:32: 8000000 INFO @ Tue, 02 Aug 2022 17:25:35: 12000000 INFO @ Tue, 02 Aug 2022 17:25:40: 17000000 INFO @ Tue, 02 Aug 2022 17:25:40: 9000000 INFO @ Tue, 02 Aug 2022 17:25:43: 13000000 INFO @ Tue, 02 Aug 2022 17:25:48: 10000000 INFO @ Tue, 02 Aug 2022 17:25:48: 18000000 INFO @ Tue, 02 Aug 2022 17:25:51: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:25:56: 11000000 INFO @ Tue, 02 Aug 2022 17:25:56: 19000000 INFO @ Tue, 02 Aug 2022 17:25:58: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 17:25:58: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 17:25:58: #1 total tags in treatment: 9244473 INFO @ Tue, 02 Aug 2022 17:25:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:25:58: #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 17:25:59: #1 tags after filtering in treatment: 7051165 INFO @ Tue, 02 Aug 2022 17:25:59: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 17:25:59: #1 finished! INFO @ Tue, 02 Aug 2022 17:25:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:25:59: 15000000 INFO @ Tue, 02 Aug 2022 17:25:59: #2 number of paired peaks: 4216 INFO @ Tue, 02 Aug 2022 17:25:59: start model_add_line... INFO @ Tue, 02 Aug 2022 17:25:59: start X-correlation... INFO @ Tue, 02 Aug 2022 17:25:59: end of X-cor INFO @ Tue, 02 Aug 2022 17:25:59: #2 finished! INFO @ Tue, 02 Aug 2022 17:25:59: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 17:25:59: #2 alternative fragment length(s) may be 1,166 bps INFO @ Tue, 02 Aug 2022 17:25:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.05_model.r WARNING @ Tue, 02 Aug 2022 17:25:59: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:25:59: #2 You may need to consider one of the other alternative d(s): 1,166 WARNING @ Tue, 02 Aug 2022 17:25:59: #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 17:25:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:26:03: 12000000 INFO @ Tue, 02 Aug 2022 17:26:07: 16000000 INFO @ Tue, 02 Aug 2022 17:26:11: 13000000 INFO @ Tue, 02 Aug 2022 17:26:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:26:15: 17000000 INFO @ Tue, 02 Aug 2022 17:26:19: 14000000 INFO @ Tue, 02 Aug 2022 17:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.05_summits.bed INFO @ Tue, 02 Aug 2022 17:26:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2046 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:26:23: 18000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:26:27: 15000000 INFO @ Tue, 02 Aug 2022 17:26:30: 19000000 INFO @ Tue, 02 Aug 2022 17:26:33: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 17:26:33: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 17:26:33: #1 total tags in treatment: 9244473 INFO @ Tue, 02 Aug 2022 17:26:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:26:33: #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 17:26:33: #1 tags after filtering in treatment: 7051165 INFO @ Tue, 02 Aug 2022 17:26:33: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 17:26:33: #1 finished! INFO @ Tue, 02 Aug 2022 17:26:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:26:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:26:34: #2 number of paired peaks: 4216 INFO @ Tue, 02 Aug 2022 17:26:34: start model_add_line... INFO @ Tue, 02 Aug 2022 17:26:34: start X-correlation... INFO @ Tue, 02 Aug 2022 17:26:34: end of X-cor INFO @ Tue, 02 Aug 2022 17:26:34: #2 finished! INFO @ Tue, 02 Aug 2022 17:26:34: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 17:26:34: #2 alternative fragment length(s) may be 1,166 bps INFO @ Tue, 02 Aug 2022 17:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.10_model.r WARNING @ Tue, 02 Aug 2022 17:26:34: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:26:34: #2 You may need to consider one of the other alternative d(s): 1,166 WARNING @ Tue, 02 Aug 2022 17:26:34: #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 17:26:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:26:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:26:35: 16000000 INFO @ Tue, 02 Aug 2022 17:26:41: 17000000 INFO @ Tue, 02 Aug 2022 17:26:48: 18000000 INFO @ Tue, 02 Aug 2022 17:26:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:26:55: 19000000 INFO @ Tue, 02 Aug 2022 17:26:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:26:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:26:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.10_summits.bed INFO @ Tue, 02 Aug 2022 17:26:56: Done! pass1 - making usageList (10 chroms): 1 millis INFO @ Tue, 02 Aug 2022 17:26:57: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 17:26:57: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 17:26:57: #1 total tags in treatment: 9244473 INFO @ Tue, 02 Aug 2022 17:26:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:26:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass2 - checking and writing primary data (744 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:26:57: #1 tags after filtering in treatment: 7051165 INFO @ Tue, 02 Aug 2022 17:26:57: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 17:26:57: #1 finished! INFO @ Tue, 02 Aug 2022 17:26:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:26:58: #2 number of paired peaks: 4216 INFO @ Tue, 02 Aug 2022 17:26:58: start model_add_line... INFO @ Tue, 02 Aug 2022 17:26:58: start X-correlation... INFO @ Tue, 02 Aug 2022 17:26:58: end of X-cor INFO @ Tue, 02 Aug 2022 17:26:58: #2 finished! INFO @ Tue, 02 Aug 2022 17:26:58: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 17:26:58: #2 alternative fragment length(s) may be 1,166 bps INFO @ Tue, 02 Aug 2022 17:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.20_model.r WARNING @ Tue, 02 Aug 2022 17:26:58: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:26:58: #2 You may need to consider one of the other alternative d(s): 1,166 WARNING @ Tue, 02 Aug 2022 17:26:58: #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 17:26:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:27:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:27:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855764/SRX10855764.20_summits.bed INFO @ Tue, 02 Aug 2022 17:27:21: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (318 records, 4 fields): 16 millis CompletedMACS2peakCalling