Job ID = 16439485 SRX = SRX9518327 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7936038 spots for SRR13070810/SRR13070810.sra Written 7936038 spots for SRR13070810/SRR13070810.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439660 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:29 7936038 reads; of these: 7936038 (100.00%) were paired; of these: 1082254 (13.64%) aligned concordantly 0 times 5322858 (67.07%) aligned concordantly exactly 1 time 1530926 (19.29%) aligned concordantly >1 times ---- 1082254 pairs aligned concordantly 0 times; of these: 144460 (13.35%) aligned discordantly 1 time ---- 937794 pairs aligned 0 times concordantly or discordantly; of these: 1875588 mates make up the pairs; of these: 1644246 (87.67%) aligned 0 times 113262 (6.04%) aligned exactly 1 time 118080 (6.30%) aligned >1 times 89.64% overall alignment rate Time searching: 00:26:30 Overall time: 00:26:30 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 8 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] 496271 / 6982111 = 0.0711 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 15:52:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.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 15:52:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:52:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:53:08: 1000000 INFO @ Tue, 02 Aug 2022 15:53:18: 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 15:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.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 15:53:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:53:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:53:28: 3000000 INFO @ Tue, 02 Aug 2022 15:53:37: 1000000 INFO @ Tue, 02 Aug 2022 15:53:40: 4000000 INFO @ Tue, 02 Aug 2022 15:53:47: 2000000 INFO @ Tue, 02 Aug 2022 15:53:50: 5000000 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 15:53:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.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 15:53:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:53:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:53:57: 3000000 INFO @ Tue, 02 Aug 2022 15:54:02: 6000000 INFO @ Tue, 02 Aug 2022 15:54:06: 1000000 INFO @ Tue, 02 Aug 2022 15:54:07: 4000000 INFO @ Tue, 02 Aug 2022 15:54:13: 7000000 INFO @ Tue, 02 Aug 2022 15:54:16: 2000000 INFO @ Tue, 02 Aug 2022 15:54:17: 5000000 INFO @ Tue, 02 Aug 2022 15:54:24: 8000000 INFO @ Tue, 02 Aug 2022 15:54:26: 3000000 INFO @ Tue, 02 Aug 2022 15:54:27: 6000000 INFO @ Tue, 02 Aug 2022 15:54:36: 9000000 INFO @ Tue, 02 Aug 2022 15:54:36: 4000000 INFO @ Tue, 02 Aug 2022 15:54:38: 7000000 INFO @ Tue, 02 Aug 2022 15:54:47: 5000000 INFO @ Tue, 02 Aug 2022 15:54:48: 10000000 INFO @ Tue, 02 Aug 2022 15:54:48: 8000000 INFO @ Tue, 02 Aug 2022 15:54:56: 6000000 INFO @ Tue, 02 Aug 2022 15:54:59: 11000000 INFO @ Tue, 02 Aug 2022 15:55:00: 9000000 INFO @ Tue, 02 Aug 2022 15:55:06: 7000000 INFO @ Tue, 02 Aug 2022 15:55:10: 12000000 INFO @ Tue, 02 Aug 2022 15:55:12: 10000000 INFO @ Tue, 02 Aug 2022 15:55:16: 8000000 INFO @ Tue, 02 Aug 2022 15:55:21: 13000000 INFO @ Tue, 02 Aug 2022 15:55:23: 11000000 INFO @ Tue, 02 Aug 2022 15:55:24: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:55:24: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:55:24: #1 total tags in treatment: 6362161 INFO @ Tue, 02 Aug 2022 15:55:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:55:24: #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 15:55:25: #1 tags after filtering in treatment: 5956022 INFO @ Tue, 02 Aug 2022 15:55:25: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 15:55:25: #1 finished! INFO @ Tue, 02 Aug 2022 15:55:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:55:25: #2 number of paired peaks: 2850 INFO @ Tue, 02 Aug 2022 15:55:25: start model_add_line... INFO @ Tue, 02 Aug 2022 15:55:25: start X-correlation... INFO @ Tue, 02 Aug 2022 15:55:25: end of X-cor INFO @ Tue, 02 Aug 2022 15:55:25: #2 finished! INFO @ Tue, 02 Aug 2022 15:55:25: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 15:55:25: #2 alternative fragment length(s) may be 192,596 bps INFO @ Tue, 02 Aug 2022 15:55:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.05_model.r WARNING @ Tue, 02 Aug 2022 15:55:25: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:55:25: #2 You may need to consider one of the other alternative d(s): 192,596 WARNING @ Tue, 02 Aug 2022 15:55:25: #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 15:55:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:55:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:55:26: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:55:34: 12000000 INFO @ Tue, 02 Aug 2022 15:55:36: 10000000 INFO @ Tue, 02 Aug 2022 15:55:45: 13000000 INFO @ Tue, 02 Aug 2022 15:55:46: 11000000 INFO @ Tue, 02 Aug 2022 15:55:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:55:48: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:55:48: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:55:48: #1 total tags in treatment: 6362161 INFO @ Tue, 02 Aug 2022 15:55:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:55:48: #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 15:55:48: #1 tags after filtering in treatment: 5956022 INFO @ Tue, 02 Aug 2022 15:55:48: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 15:55:48: #1 finished! INFO @ Tue, 02 Aug 2022 15:55:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:55:49: #2 number of paired peaks: 2850 INFO @ Tue, 02 Aug 2022 15:55:49: start model_add_line... INFO @ Tue, 02 Aug 2022 15:55:49: start X-correlation... INFO @ Tue, 02 Aug 2022 15:55:49: end of X-cor INFO @ Tue, 02 Aug 2022 15:55:49: #2 finished! INFO @ Tue, 02 Aug 2022 15:55:49: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 15:55:49: #2 alternative fragment length(s) may be 192,596 bps INFO @ Tue, 02 Aug 2022 15:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.10_model.r WARNING @ Tue, 02 Aug 2022 15:55:49: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:55:49: #2 You may need to consider one of the other alternative d(s): 192,596 WARNING @ Tue, 02 Aug 2022 15:55:49: #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 15:55:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:55:56: 12000000 INFO @ Tue, 02 Aug 2022 15:55:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:55:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:55:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.05_summits.bed INFO @ Tue, 02 Aug 2022 15:55:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3254 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:56:06: 13000000 INFO @ Tue, 02 Aug 2022 15:56:08: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:56:08: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:56:08: #1 total tags in treatment: 6362161 INFO @ Tue, 02 Aug 2022 15:56:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:56:08: #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 15:56:08: #1 tags after filtering in treatment: 5956022 INFO @ Tue, 02 Aug 2022 15:56:08: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 15:56:08: #1 finished! INFO @ Tue, 02 Aug 2022 15:56:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:56:08: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:56:09: #2 number of paired peaks: 2850 INFO @ Tue, 02 Aug 2022 15:56:09: start model_add_line... INFO @ Tue, 02 Aug 2022 15:56:09: start X-correlation... INFO @ Tue, 02 Aug 2022 15:56:09: end of X-cor INFO @ Tue, 02 Aug 2022 15:56:09: #2 finished! INFO @ Tue, 02 Aug 2022 15:56:09: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 15:56:09: #2 alternative fragment length(s) may be 192,596 bps INFO @ Tue, 02 Aug 2022 15:56:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.20_model.r WARNING @ Tue, 02 Aug 2022 15:56:09: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:56:09: #2 You may need to consider one of the other alternative d(s): 192,596 WARNING @ Tue, 02 Aug 2022 15:56:09: #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 15:56:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:56:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:56:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:56:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:56:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.10_summits.bed INFO @ Tue, 02 Aug 2022 15:56:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2245 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:56:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:56:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:56:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:56:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518327/SRX9518327.20_summits.bed INFO @ Tue, 02 Aug 2022 15:56:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1482 records, 4 fields): 19 millis CompletedMACS2peakCalling