Job ID = 16439426 SRX = SRX11245083 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:08:22 prefetch.2.10.7: 1) Downloading 'SRR14932348'... 2022-08-02T06:08:22 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:09:26 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:09:26 prefetch.2.10.7: 1) 'SRR14932348' was downloaded successfully 2022-08-02T06:09:26 prefetch.2.10.7: 'SRR14932348' has 0 unresolved dependencies Read 28424139 spots for SRR14932348/SRR14932348.sra Written 28424139 spots for SRR14932348/SRR14932348.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439974 ("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: 01:10:29 28424139 reads; of these: 28424139 (100.00%) were paired; of these: 18687525 (65.75%) aligned concordantly 0 times 8084737 (28.44%) aligned concordantly exactly 1 time 1651877 (5.81%) aligned concordantly >1 times ---- 18687525 pairs aligned concordantly 0 times; of these: 1835198 (9.82%) aligned discordantly 1 time ---- 16852327 pairs aligned 0 times concordantly or discordantly; of these: 33704654 mates make up the pairs; of these: 32396320 (96.12%) aligned 0 times 482590 (1.43%) aligned exactly 1 time 825744 (2.45%) aligned >1 times 43.01% overall alignment rate Time searching: 01:10:29 Overall time: 01:10:29 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] 4331430 / 11539110 = 0.3754 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 16:38:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.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 16:38:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:38:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:38:18: 1000000 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 16:38:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.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 16:38:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:38:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:38:34: 2000000 INFO @ Tue, 02 Aug 2022 16:38:49: 1000000 INFO @ Tue, 02 Aug 2022 16:38:50: 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 16:39:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.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 16:39:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:39:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:39:04: 2000000 INFO @ Tue, 02 Aug 2022 16:39:05: 4000000 INFO @ Tue, 02 Aug 2022 16:39:19: 1000000 INFO @ Tue, 02 Aug 2022 16:39:20: 3000000 INFO @ Tue, 02 Aug 2022 16:39:21: 5000000 INFO @ Tue, 02 Aug 2022 16:39:33: 2000000 INFO @ Tue, 02 Aug 2022 16:39:36: 4000000 INFO @ Tue, 02 Aug 2022 16:39:38: 6000000 INFO @ Tue, 02 Aug 2022 16:39:45: 3000000 INFO @ Tue, 02 Aug 2022 16:39:52: 5000000 INFO @ Tue, 02 Aug 2022 16:39:54: 7000000 INFO @ Tue, 02 Aug 2022 16:39:58: 4000000 INFO @ Tue, 02 Aug 2022 16:40:08: 6000000 INFO @ Tue, 02 Aug 2022 16:40:09: 8000000 INFO @ Tue, 02 Aug 2022 16:40:10: 5000000 INFO @ Tue, 02 Aug 2022 16:40:22: 6000000 INFO @ Tue, 02 Aug 2022 16:40:24: 7000000 INFO @ Tue, 02 Aug 2022 16:40:24: 9000000 INFO @ Tue, 02 Aug 2022 16:40:34: 7000000 INFO @ Tue, 02 Aug 2022 16:40:39: 8000000 INFO @ Tue, 02 Aug 2022 16:40:39: 10000000 INFO @ Tue, 02 Aug 2022 16:40:47: 8000000 INFO @ Tue, 02 Aug 2022 16:40:54: 9000000 INFO @ Tue, 02 Aug 2022 16:40:54: 11000000 INFO @ Tue, 02 Aug 2022 16:40:59: 9000000 INFO @ Tue, 02 Aug 2022 16:41:07: 10000000 INFO @ Tue, 02 Aug 2022 16:41:08: 12000000 INFO @ Tue, 02 Aug 2022 16:41:12: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:41:22: 11000000 INFO @ Tue, 02 Aug 2022 16:41:24: 11000000 INFO @ Tue, 02 Aug 2022 16:41:25: 13000000 INFO @ Tue, 02 Aug 2022 16:41:37: 12000000 INFO @ Tue, 02 Aug 2022 16:41:37: 12000000 INFO @ Tue, 02 Aug 2022 16:41:42: 14000000 INFO @ Tue, 02 Aug 2022 16:41:49: 13000000 INFO @ Tue, 02 Aug 2022 16:41:54: 13000000 INFO @ Tue, 02 Aug 2022 16:41:58: 15000000 INFO @ Tue, 02 Aug 2022 16:42:02: 14000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:42:11: 14000000 INFO @ Tue, 02 Aug 2022 16:42:12: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:42:12: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:42:12: #1 total tags in treatment: 6129370 INFO @ Tue, 02 Aug 2022 16:42:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:42:12: #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 16:42:12: #1 tags after filtering in treatment: 5945819 INFO @ Tue, 02 Aug 2022 16:42:12: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:42:12: #1 finished! INFO @ Tue, 02 Aug 2022 16:42:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:42:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:42:12: #2 number of paired peaks: 175 WARNING @ Tue, 02 Aug 2022 16:42:12: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 02 Aug 2022 16:42:12: start model_add_line... INFO @ Tue, 02 Aug 2022 16:42:12: start X-correlation... INFO @ Tue, 02 Aug 2022 16:42:12: end of X-cor INFO @ Tue, 02 Aug 2022 16:42:12: #2 finished! INFO @ Tue, 02 Aug 2022 16:42:12: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 16:42:13: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 16:42:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.05_model.r WARNING @ Tue, 02 Aug 2022 16:42:13: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:42:13: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Tue, 02 Aug 2022 16:42:13: #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 16:42:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:42:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:42:14: 15000000 INFO @ Tue, 02 Aug 2022 16:42:25: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:42:25: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:42:25: #1 total tags in treatment: 6129370 INFO @ Tue, 02 Aug 2022 16:42:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:42:25: #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 16:42:25: #1 tags after filtering in treatment: 5945819 INFO @ Tue, 02 Aug 2022 16:42:25: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:42:25: #1 finished! INFO @ Tue, 02 Aug 2022 16:42:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:42:26: #2 number of paired peaks: 175 WARNING @ Tue, 02 Aug 2022 16:42:26: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 02 Aug 2022 16:42:26: start model_add_line... INFO @ Tue, 02 Aug 2022 16:42:26: start X-correlation... INFO @ Tue, 02 Aug 2022 16:42:26: end of X-cor INFO @ Tue, 02 Aug 2022 16:42:26: #2 finished! INFO @ Tue, 02 Aug 2022 16:42:26: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 16:42:26: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 16:42:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.20_model.r WARNING @ Tue, 02 Aug 2022 16:42:26: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:42:26: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Tue, 02 Aug 2022 16:42:26: #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 16:42:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:42:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:42:26: 15000000 INFO @ Tue, 02 Aug 2022 16:42:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:42:37: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:42:37: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:42:37: #1 total tags in treatment: 6129370 INFO @ Tue, 02 Aug 2022 16:42:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:42:37: #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 16:42:38: #1 tags after filtering in treatment: 5945819 INFO @ Tue, 02 Aug 2022 16:42:38: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:42:38: #1 finished! INFO @ Tue, 02 Aug 2022 16:42:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:42:38: #2 number of paired peaks: 175 WARNING @ Tue, 02 Aug 2022 16:42:38: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 02 Aug 2022 16:42:38: start model_add_line... INFO @ Tue, 02 Aug 2022 16:42:38: start X-correlation... INFO @ Tue, 02 Aug 2022 16:42:38: end of X-cor INFO @ Tue, 02 Aug 2022 16:42:38: #2 finished! INFO @ Tue, 02 Aug 2022 16:42:38: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 16:42:38: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 16:42:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.10_model.r WARNING @ Tue, 02 Aug 2022 16:42:38: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:42:38: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Tue, 02 Aug 2022 16:42:38: #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 16:42:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:42:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:42:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:42:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:42:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.05_summits.bed INFO @ Tue, 02 Aug 2022 16:42:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1170 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:42:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:42:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:42:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.20_summits.bed INFO @ Tue, 02 Aug 2022 16:42:55: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (287 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:42:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:43:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:43:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:43:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245083/SRX11245083.10_summits.bed INFO @ Tue, 02 Aug 2022 16:43:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 37 millis CompletedMACS2peakCalling