Job ID = 16440071 SRX = SRX10855783 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21975501 spots for SRR14509970/SRR14509970.sra Written 21975501 spots for SRR14509970/SRR14509970.sra fastq に変換しました。 bowtie でマッピング中... Your job 16441139 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:39:06 21975501 reads; of these: 21975501 (100.00%) were paired; of these: 1569166 (7.14%) aligned concordantly 0 times 14160022 (64.44%) aligned concordantly exactly 1 time 6246313 (28.42%) aligned concordantly >1 times ---- 1569166 pairs aligned concordantly 0 times; of these: 299009 (19.06%) aligned discordantly 1 time ---- 1270157 pairs aligned 0 times concordantly or discordantly; of these: 2540314 mates make up the pairs; of these: 1765901 (69.52%) aligned 0 times 468136 (18.43%) aligned exactly 1 time 306277 (12.06%) aligned >1 times 95.98% overall alignment rate Time searching: 01:39:07 Overall time: 01:39:07 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 20 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] 10773312 / 20622151 = 0.5224 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 19:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.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 19:01:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 19:01:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 19:01:45: 1000000 INFO @ Tue, 02 Aug 2022 19:01:56: 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 19:02:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.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 19:02:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 19:02:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 19:02:07: 3000000 INFO @ Tue, 02 Aug 2022 19:02:16: 1000000 INFO @ Tue, 02 Aug 2022 19:02:18: 4000000 INFO @ Tue, 02 Aug 2022 19:02:29: 5000000 INFO @ Tue, 02 Aug 2022 19:02:30: 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 19:02:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.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 19:02:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 19:02:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 19:02:40: 6000000 INFO @ Tue, 02 Aug 2022 19:02:43: 3000000 INFO @ Tue, 02 Aug 2022 19:02:46: 1000000 INFO @ Tue, 02 Aug 2022 19:02:50: 7000000 INFO @ Tue, 02 Aug 2022 19:02:57: 4000000 INFO @ Tue, 02 Aug 2022 19:03:00: 2000000 INFO @ Tue, 02 Aug 2022 19:03:00: 8000000 INFO @ Tue, 02 Aug 2022 19:03:10: 9000000 INFO @ Tue, 02 Aug 2022 19:03:11: 5000000 INFO @ Tue, 02 Aug 2022 19:03:14: 3000000 INFO @ Tue, 02 Aug 2022 19:03:20: 10000000 INFO @ Tue, 02 Aug 2022 19:03:23: 6000000 INFO @ Tue, 02 Aug 2022 19:03:27: 4000000 INFO @ Tue, 02 Aug 2022 19:03:30: 11000000 INFO @ Tue, 02 Aug 2022 19:03:35: 7000000 INFO @ Tue, 02 Aug 2022 19:03:40: 5000000 INFO @ Tue, 02 Aug 2022 19:03:40: 12000000 INFO @ Tue, 02 Aug 2022 19:03:46: 8000000 INFO @ Tue, 02 Aug 2022 19:03:50: 13000000 INFO @ Tue, 02 Aug 2022 19:03:53: 6000000 INFO @ Tue, 02 Aug 2022 19:03:57: 9000000 INFO @ Tue, 02 Aug 2022 19:04:00: 14000000 INFO @ Tue, 02 Aug 2022 19:04:06: 7000000 INFO @ Tue, 02 Aug 2022 19:04:07: 10000000 INFO @ Tue, 02 Aug 2022 19:04:11: 15000000 INFO @ Tue, 02 Aug 2022 19:04:19: 11000000 INFO @ Tue, 02 Aug 2022 19:04:19: 8000000 INFO @ Tue, 02 Aug 2022 19:04:20: 16000000 INFO @ Tue, 02 Aug 2022 19:04:29: 12000000 INFO @ Tue, 02 Aug 2022 19:04:31: 17000000 INFO @ Tue, 02 Aug 2022 19:04:33: 9000000 INFO @ Tue, 02 Aug 2022 19:04:41: 13000000 INFO @ Tue, 02 Aug 2022 19:04:41: 18000000 INFO @ Tue, 02 Aug 2022 19:04:46: 10000000 INFO @ Tue, 02 Aug 2022 19:04:52: 19000000 INFO @ Tue, 02 Aug 2022 19:04:52: 14000000 INFO @ Tue, 02 Aug 2022 19:04:59: 11000000 INFO @ Tue, 02 Aug 2022 19:05:02: 20000000 INFO @ Tue, 02 Aug 2022 19:05:04: 15000000 INFO @ Tue, 02 Aug 2022 19:05:09: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 19:05:09: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 19:05:09: #1 total tags in treatment: 9746356 INFO @ Tue, 02 Aug 2022 19:05:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:05:09: #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 19:05:09: #1 tags after filtering in treatment: 7800612 INFO @ Tue, 02 Aug 2022 19:05:09: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 02 Aug 2022 19:05:09: #1 finished! INFO @ Tue, 02 Aug 2022 19:05:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:05:10: #2 number of paired peaks: 1839 INFO @ Tue, 02 Aug 2022 19:05:10: start model_add_line... INFO @ Tue, 02 Aug 2022 19:05:11: start X-correlation... INFO @ Tue, 02 Aug 2022 19:05:11: end of X-cor INFO @ Tue, 02 Aug 2022 19:05:11: #2 finished! INFO @ Tue, 02 Aug 2022 19:05:11: #2 predicted fragment length is 165 bps INFO @ Tue, 02 Aug 2022 19:05:11: #2 alternative fragment length(s) may be 3,165 bps INFO @ Tue, 02 Aug 2022 19:05:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.05_model.r WARNING @ Tue, 02 Aug 2022 19:05:11: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:05:11: #2 You may need to consider one of the other alternative d(s): 3,165 WARNING @ Tue, 02 Aug 2022 19:05:11: #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 19:05:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:05:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:05:12: 12000000 INFO @ Tue, 02 Aug 2022 19:05:16: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 19:05:25: 13000000 INFO @ Tue, 02 Aug 2022 19:05:27: 17000000 INFO @ Tue, 02 Aug 2022 19:05:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:05:38: 18000000 INFO @ Tue, 02 Aug 2022 19:05:39: 14000000 INFO @ Tue, 02 Aug 2022 19:05:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.05_peaks.xls INFO @ Tue, 02 Aug 2022 19:05:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:05:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.05_summits.bed INFO @ Tue, 02 Aug 2022 19:05:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3530 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 19:05:50: 19000000 INFO @ Tue, 02 Aug 2022 19:05:52: 15000000 INFO @ Tue, 02 Aug 2022 19:06:00: 20000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 19:06:05: 16000000 INFO @ Tue, 02 Aug 2022 19:06:08: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 19:06:08: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 19:06:08: #1 total tags in treatment: 9746356 INFO @ Tue, 02 Aug 2022 19:06:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:06:08: #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 19:06:08: #1 tags after filtering in treatment: 7800612 INFO @ Tue, 02 Aug 2022 19:06:08: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 02 Aug 2022 19:06:08: #1 finished! INFO @ Tue, 02 Aug 2022 19:06:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:06:09: #2 number of paired peaks: 1839 INFO @ Tue, 02 Aug 2022 19:06:09: start model_add_line... INFO @ Tue, 02 Aug 2022 19:06:09: start X-correlation... INFO @ Tue, 02 Aug 2022 19:06:09: end of X-cor INFO @ Tue, 02 Aug 2022 19:06:09: #2 finished! INFO @ Tue, 02 Aug 2022 19:06:09: #2 predicted fragment length is 165 bps INFO @ Tue, 02 Aug 2022 19:06:09: #2 alternative fragment length(s) may be 3,165 bps INFO @ Tue, 02 Aug 2022 19:06:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.10_model.r WARNING @ Tue, 02 Aug 2022 19:06:09: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:06:09: #2 You may need to consider one of the other alternative d(s): 3,165 WARNING @ Tue, 02 Aug 2022 19:06:09: #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 19:06:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:06:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:06:18: 17000000 INFO @ Tue, 02 Aug 2022 19:06:30: 18000000 INFO @ Tue, 02 Aug 2022 19:06:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:06:43: 19000000 INFO @ Tue, 02 Aug 2022 19:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.10_peaks.xls INFO @ Tue, 02 Aug 2022 19:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.10_summits.bed INFO @ Tue, 02 Aug 2022 19:06:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1222 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 19:06:56: 20000000 INFO @ Tue, 02 Aug 2022 19:07:04: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 19:07:04: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 19:07:04: #1 total tags in treatment: 9746356 INFO @ Tue, 02 Aug 2022 19:07:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:07:04: #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 19:07:04: #1 tags after filtering in treatment: 7800612 INFO @ Tue, 02 Aug 2022 19:07:04: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 02 Aug 2022 19:07:04: #1 finished! INFO @ Tue, 02 Aug 2022 19:07:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:07:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:07:05: #2 number of paired peaks: 1839 INFO @ Tue, 02 Aug 2022 19:07:05: start model_add_line... INFO @ Tue, 02 Aug 2022 19:07:05: start X-correlation... INFO @ Tue, 02 Aug 2022 19:07:05: end of X-cor INFO @ Tue, 02 Aug 2022 19:07:05: #2 finished! INFO @ Tue, 02 Aug 2022 19:07:05: #2 predicted fragment length is 165 bps INFO @ Tue, 02 Aug 2022 19:07:05: #2 alternative fragment length(s) may be 3,165 bps INFO @ Tue, 02 Aug 2022 19:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.20_model.r WARNING @ Tue, 02 Aug 2022 19:07:06: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:07:06: #2 You may need to consider one of the other alternative d(s): 3,165 WARNING @ Tue, 02 Aug 2022 19:07:06: #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 19:07:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:07:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.20_peaks.xls INFO @ Tue, 02 Aug 2022 19:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855783/SRX10855783.20_summits.bed INFO @ Tue, 02 Aug 2022 19:07:44: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 4 millis CompletedMACS2peakCalling