Job ID = 16439722 SRX = SRX8369904 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26226680 spots for SRR11818940/SRR11818940.sra Written 26226680 spots for SRR11818940/SRR11818940.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440092 ("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: 00:53:35 26226680 reads; of these: 26226680 (100.00%) were paired; of these: 18873562 (71.96%) aligned concordantly 0 times 6306307 (24.05%) aligned concordantly exactly 1 time 1046811 (3.99%) aligned concordantly >1 times ---- 18873562 pairs aligned concordantly 0 times; of these: 2326369 (12.33%) aligned discordantly 1 time ---- 16547193 pairs aligned 0 times concordantly or discordantly; of these: 33094386 mates make up the pairs; of these: 31293975 (94.56%) aligned 0 times 904866 (2.73%) aligned exactly 1 time 895545 (2.71%) aligned >1 times 40.34% overall alignment rate Time searching: 00:53:35 Overall time: 00:53:35 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 16 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] 1130378 / 9626920 = 0.1174 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 17:11:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.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 17:11:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:11:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:12:05: 1000000 INFO @ Tue, 02 Aug 2022 17:12:17: 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 17:12:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.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 17:12:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:12:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:12:28: 3000000 INFO @ Tue, 02 Aug 2022 17:12:36: 1000000 INFO @ Tue, 02 Aug 2022 17:12:39: 4000000 INFO @ Tue, 02 Aug 2022 17:12:50: 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 17:12:51: 5000000 INFO @ Tue, 02 Aug 2022 17:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.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 17:12:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:12:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:13:03: 3000000 INFO @ Tue, 02 Aug 2022 17:13:03: 6000000 INFO @ Tue, 02 Aug 2022 17:13:07: 1000000 INFO @ Tue, 02 Aug 2022 17:13:15: 7000000 INFO @ Tue, 02 Aug 2022 17:13:17: 4000000 INFO @ Tue, 02 Aug 2022 17:13:20: 2000000 INFO @ Tue, 02 Aug 2022 17:13:27: 8000000 INFO @ Tue, 02 Aug 2022 17:13:30: 5000000 INFO @ Tue, 02 Aug 2022 17:13:34: 3000000 INFO @ Tue, 02 Aug 2022 17:13:40: 9000000 INFO @ Tue, 02 Aug 2022 17:13:44: 6000000 INFO @ Tue, 02 Aug 2022 17:13:48: 4000000 INFO @ Tue, 02 Aug 2022 17:13:52: 10000000 INFO @ Tue, 02 Aug 2022 17:13:57: 7000000 INFO @ Tue, 02 Aug 2022 17:14:01: 5000000 INFO @ Tue, 02 Aug 2022 17:14:04: 11000000 INFO @ Tue, 02 Aug 2022 17:14:11: 8000000 INFO @ Tue, 02 Aug 2022 17:14:15: 6000000 INFO @ Tue, 02 Aug 2022 17:14:16: 12000000 INFO @ Tue, 02 Aug 2022 17:14:26: 9000000 INFO @ Tue, 02 Aug 2022 17:14:28: 13000000 INFO @ Tue, 02 Aug 2022 17:14:28: 7000000 INFO @ Tue, 02 Aug 2022 17:14:39: 10000000 INFO @ Tue, 02 Aug 2022 17:14:40: 14000000 INFO @ Tue, 02 Aug 2022 17:14:42: 8000000 INFO @ Tue, 02 Aug 2022 17:14:52: 15000000 INFO @ Tue, 02 Aug 2022 17:14:52: 11000000 INFO @ Tue, 02 Aug 2022 17:14:55: 9000000 INFO @ Tue, 02 Aug 2022 17:15:04: 16000000 INFO @ Tue, 02 Aug 2022 17:15:06: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:15:09: 10000000 INFO @ Tue, 02 Aug 2022 17:15:17: 17000000 INFO @ Tue, 02 Aug 2022 17:15:20: 13000000 INFO @ Tue, 02 Aug 2022 17:15:22: 11000000 INFO @ Tue, 02 Aug 2022 17:15:30: 18000000 INFO @ Tue, 02 Aug 2022 17:15:34: 14000000 INFO @ Tue, 02 Aug 2022 17:15:36: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:15:41: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:15:41: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:15:41: #1 total tags in treatment: 6461151 INFO @ Tue, 02 Aug 2022 17:15:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:15:41: #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 17:15:41: #1 tags after filtering in treatment: 4631501 INFO @ Tue, 02 Aug 2022 17:15:41: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 17:15:41: #1 finished! INFO @ Tue, 02 Aug 2022 17:15:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:15:42: #2 number of paired peaks: 6556 INFO @ Tue, 02 Aug 2022 17:15:42: start model_add_line... INFO @ Tue, 02 Aug 2022 17:15:42: start X-correlation... INFO @ Tue, 02 Aug 2022 17:15:42: end of X-cor INFO @ Tue, 02 Aug 2022 17:15:42: #2 finished! INFO @ Tue, 02 Aug 2022 17:15:42: #2 predicted fragment length is 217 bps INFO @ Tue, 02 Aug 2022 17:15:42: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 02 Aug 2022 17:15:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.05_model.r WARNING @ Tue, 02 Aug 2022 17:15:42: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:15:42: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 02 Aug 2022 17:15:42: #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 17:15:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:15:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:15:47: 15000000 INFO @ Tue, 02 Aug 2022 17:15:51: 13000000 INFO @ Tue, 02 Aug 2022 17:15:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:16:01: 16000000 INFO @ Tue, 02 Aug 2022 17:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.05_summits.bed INFO @ Tue, 02 Aug 2022 17:16:01: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10389 records, 4 fields): 73 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:16:05: 14000000 INFO @ Tue, 02 Aug 2022 17:16:15: 17000000 INFO @ Tue, 02 Aug 2022 17:16:19: 15000000 INFO @ Tue, 02 Aug 2022 17:16:29: 18000000 INFO @ Tue, 02 Aug 2022 17:16:34: 16000000 INFO @ Tue, 02 Aug 2022 17:16:42: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:16:42: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:16:42: #1 total tags in treatment: 6461151 INFO @ Tue, 02 Aug 2022 17:16:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:16:42: #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 17:16:42: #1 tags after filtering in treatment: 4631501 INFO @ Tue, 02 Aug 2022 17:16:42: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 17:16:42: #1 finished! INFO @ Tue, 02 Aug 2022 17:16:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:16:43: #2 number of paired peaks: 6556 INFO @ Tue, 02 Aug 2022 17:16:43: start model_add_line... INFO @ Tue, 02 Aug 2022 17:16:43: start X-correlation... INFO @ Tue, 02 Aug 2022 17:16:43: end of X-cor INFO @ Tue, 02 Aug 2022 17:16:43: #2 finished! INFO @ Tue, 02 Aug 2022 17:16:43: #2 predicted fragment length is 217 bps INFO @ Tue, 02 Aug 2022 17:16:43: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 02 Aug 2022 17:16:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.10_model.r WARNING @ Tue, 02 Aug 2022 17:16:43: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:16:43: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 02 Aug 2022 17:16:43: #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 17:16:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:16:48: 17000000 INFO @ Tue, 02 Aug 2022 17:16:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:17:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:17:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.10_summits.bed INFO @ Tue, 02 Aug 2022 17:17:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6990 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:17:02: 18000000 INFO @ Tue, 02 Aug 2022 17:17:15: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:17:15: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:17:15: #1 total tags in treatment: 6461151 INFO @ Tue, 02 Aug 2022 17:17:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:17:15: #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 17:17:15: #1 tags after filtering in treatment: 4631501 INFO @ Tue, 02 Aug 2022 17:17:15: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 17:17:15: #1 finished! INFO @ Tue, 02 Aug 2022 17:17:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:17:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:17:16: #2 number of paired peaks: 6556 INFO @ Tue, 02 Aug 2022 17:17:16: start model_add_line... INFO @ Tue, 02 Aug 2022 17:17:16: start X-correlation... INFO @ Tue, 02 Aug 2022 17:17:16: end of X-cor INFO @ Tue, 02 Aug 2022 17:17:16: #2 finished! INFO @ Tue, 02 Aug 2022 17:17:16: #2 predicted fragment length is 217 bps INFO @ Tue, 02 Aug 2022 17:17:16: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 02 Aug 2022 17:17:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.20_model.r WARNING @ Tue, 02 Aug 2022 17:17:16: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:17:16: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 02 Aug 2022 17:17:16: #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 17:17:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:17:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:17:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:17:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:17:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:17:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8369904/SRX8369904.20_summits.bed INFO @ Tue, 02 Aug 2022 17:17:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3601 records, 4 fields): 150 millis CompletedMACS2peakCalling