Job ID = 16439329 SRX = SRX14232167 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21279368 spots for SRR18080651/SRR18080651.sra Written 21279368 spots for SRR18080651/SRR18080651.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440095 ("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: 02:03:11 21279368 reads; of these: 21279368 (100.00%) were paired; of these: 6693547 (31.46%) aligned concordantly 0 times 9008338 (42.33%) aligned concordantly exactly 1 time 5577483 (26.21%) aligned concordantly >1 times ---- 6693547 pairs aligned concordantly 0 times; of these: 1527464 (22.82%) aligned discordantly 1 time ---- 5166083 pairs aligned 0 times concordantly or discordantly; of these: 10332166 mates make up the pairs; of these: 7605091 (73.61%) aligned 0 times 408587 (3.95%) aligned exactly 1 time 2318488 (22.44%) aligned >1 times 82.13% overall alignment rate Time searching: 02:03:13 Overall time: 02:03:13 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 28 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] 2992978 / 15986893 = 0.1872 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 17:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.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 17:14:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:14:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:14:25: 1000000 INFO @ Tue, 02 Aug 2022 17:14:33: 2000000 INFO @ Tue, 02 Aug 2022 17:14:40: 3000000 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 17:14:47: 4000000 INFO @ Tue, 02 Aug 2022 17:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.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 17:14:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:14:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:14:55: 5000000 INFO @ Tue, 02 Aug 2022 17:15:00: 1000000 INFO @ Tue, 02 Aug 2022 17:15:04: 6000000 INFO @ Tue, 02 Aug 2022 17:15:09: 2000000 INFO @ Tue, 02 Aug 2022 17:15:12: 7000000 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 17:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.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 17:15:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:15:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:15:19: 3000000 INFO @ Tue, 02 Aug 2022 17:15:21: 8000000 INFO @ Tue, 02 Aug 2022 17:15:27: 1000000 INFO @ Tue, 02 Aug 2022 17:15:28: 4000000 INFO @ Tue, 02 Aug 2022 17:15:30: 9000000 INFO @ Tue, 02 Aug 2022 17:15:36: 2000000 INFO @ Tue, 02 Aug 2022 17:15:38: 5000000 INFO @ Tue, 02 Aug 2022 17:15:39: 10000000 INFO @ Tue, 02 Aug 2022 17:15:45: 3000000 INFO @ Tue, 02 Aug 2022 17:15:47: 11000000 INFO @ Tue, 02 Aug 2022 17:15:47: 6000000 INFO @ Tue, 02 Aug 2022 17:15:54: 4000000 INFO @ Tue, 02 Aug 2022 17:15:56: 12000000 INFO @ Tue, 02 Aug 2022 17:15:57: 7000000 INFO @ Tue, 02 Aug 2022 17:16:03: 5000000 INFO @ Tue, 02 Aug 2022 17:16:05: 13000000 INFO @ Tue, 02 Aug 2022 17:16:06: 8000000 INFO @ Tue, 02 Aug 2022 17:16:11: 6000000 INFO @ Tue, 02 Aug 2022 17:16:14: 14000000 INFO @ Tue, 02 Aug 2022 17:16:16: 9000000 INFO @ Tue, 02 Aug 2022 17:16:20: 7000000 INFO @ Tue, 02 Aug 2022 17:16:22: 15000000 INFO @ Tue, 02 Aug 2022 17:16:26: 10000000 INFO @ Tue, 02 Aug 2022 17:16:29: 8000000 INFO @ Tue, 02 Aug 2022 17:16:31: 16000000 INFO @ Tue, 02 Aug 2022 17:16:35: 11000000 INFO @ Tue, 02 Aug 2022 17:16:38: 9000000 INFO @ Tue, 02 Aug 2022 17:16:39: 17000000 INFO @ Tue, 02 Aug 2022 17:16:44: 12000000 INFO @ Tue, 02 Aug 2022 17:16:46: 10000000 INFO @ Tue, 02 Aug 2022 17:16:48: 18000000 INFO @ Tue, 02 Aug 2022 17:16:54: 13000000 INFO @ Tue, 02 Aug 2022 17:16:55: 11000000 INFO @ Tue, 02 Aug 2022 17:16:56: 19000000 INFO @ Tue, 02 Aug 2022 17:17:04: 14000000 INFO @ Tue, 02 Aug 2022 17:17:04: 12000000 INFO @ Tue, 02 Aug 2022 17:17:05: 20000000 INFO @ Tue, 02 Aug 2022 17:17:13: 13000000 INFO @ Tue, 02 Aug 2022 17:17:13: 15000000 INFO @ Tue, 02 Aug 2022 17:17:14: 21000000 INFO @ Tue, 02 Aug 2022 17:17:21: 14000000 INFO @ Tue, 02 Aug 2022 17:17:22: 22000000 INFO @ Tue, 02 Aug 2022 17:17:23: 16000000 INFO @ Tue, 02 Aug 2022 17:17:30: 15000000 INFO @ Tue, 02 Aug 2022 17:17:30: 23000000 INFO @ Tue, 02 Aug 2022 17:17:32: 17000000 INFO @ Tue, 02 Aug 2022 17:17:38: 16000000 INFO @ Tue, 02 Aug 2022 17:17:38: 24000000 INFO @ Tue, 02 Aug 2022 17:17:41: 18000000 INFO @ Tue, 02 Aug 2022 17:17:47: 25000000 INFO @ Tue, 02 Aug 2022 17:17:47: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:17:51: 19000000 INFO @ Tue, 02 Aug 2022 17:17:55: 26000000 INFO @ Tue, 02 Aug 2022 17:17:56: 18000000 INFO @ Tue, 02 Aug 2022 17:18:00: 20000000 INFO @ Tue, 02 Aug 2022 17:18:04: 27000000 INFO @ Tue, 02 Aug 2022 17:18:04: 19000000 INFO @ Tue, 02 Aug 2022 17:18:09: 21000000 INFO @ Tue, 02 Aug 2022 17:18:13: 28000000 INFO @ Tue, 02 Aug 2022 17:18:13: 20000000 INFO @ Tue, 02 Aug 2022 17:18:19: 22000000 INFO @ Tue, 02 Aug 2022 17:18:21: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:18:21: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:18:21: #1 total tags in treatment: 11868846 INFO @ Tue, 02 Aug 2022 17:18:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:18:21: #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 17:18:21: #1 tags after filtering in treatment: 9310581 INFO @ Tue, 02 Aug 2022 17:18:21: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 17:18:21: #1 finished! INFO @ Tue, 02 Aug 2022 17:18:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:18:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:18:22: 21000000 INFO @ Tue, 02 Aug 2022 17:18:22: #2 number of paired peaks: 2441 INFO @ Tue, 02 Aug 2022 17:18:22: start model_add_line... INFO @ Tue, 02 Aug 2022 17:18:22: start X-correlation... INFO @ Tue, 02 Aug 2022 17:18:22: end of X-cor INFO @ Tue, 02 Aug 2022 17:18:22: #2 finished! INFO @ Tue, 02 Aug 2022 17:18:22: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 17:18:22: #2 alternative fragment length(s) may be 191 bps INFO @ Tue, 02 Aug 2022 17:18:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.05_model.r WARNING @ Tue, 02 Aug 2022 17:18:22: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:18:22: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Tue, 02 Aug 2022 17:18:22: #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 17:18:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:18:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:18:28: 23000000 INFO @ Tue, 02 Aug 2022 17:18:30: 22000000 INFO @ Tue, 02 Aug 2022 17:18:37: 24000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:18:38: 23000000 INFO @ Tue, 02 Aug 2022 17:18:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:18:46: 24000000 INFO @ Tue, 02 Aug 2022 17:18:46: 25000000 INFO @ Tue, 02 Aug 2022 17:18:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:18:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:18:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.05_summits.bed INFO @ Tue, 02 Aug 2022 17:18:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5784 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:18:55: 25000000 INFO @ Tue, 02 Aug 2022 17:18:56: 26000000 INFO @ Tue, 02 Aug 2022 17:19:03: 26000000 INFO @ Tue, 02 Aug 2022 17:19:05: 27000000 INFO @ Tue, 02 Aug 2022 17:19:12: 27000000 INFO @ Tue, 02 Aug 2022 17:19:15: 28000000 INFO @ Tue, 02 Aug 2022 17:19:21: 28000000 INFO @ Tue, 02 Aug 2022 17:19:24: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:19:24: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:19:24: #1 total tags in treatment: 11868846 INFO @ Tue, 02 Aug 2022 17:19:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:19:24: #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 17:19:24: #1 tags after filtering in treatment: 9310581 INFO @ Tue, 02 Aug 2022 17:19:24: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 17:19:24: #1 finished! INFO @ Tue, 02 Aug 2022 17:19:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:19:25: #2 number of paired peaks: 2441 INFO @ Tue, 02 Aug 2022 17:19:25: start model_add_line... INFO @ Tue, 02 Aug 2022 17:19:25: start X-correlation... INFO @ Tue, 02 Aug 2022 17:19:25: end of X-cor INFO @ Tue, 02 Aug 2022 17:19:25: #2 finished! INFO @ Tue, 02 Aug 2022 17:19:25: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 17:19:25: #2 alternative fragment length(s) may be 191 bps INFO @ Tue, 02 Aug 2022 17:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.10_model.r WARNING @ Tue, 02 Aug 2022 17:19:25: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:19:25: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Tue, 02 Aug 2022 17:19:25: #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 17:19:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:19:29: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:19:29: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:19:29: #1 total tags in treatment: 11868846 INFO @ Tue, 02 Aug 2022 17:19:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:19:29: #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 17:19:29: #1 tags after filtering in treatment: 9310581 INFO @ Tue, 02 Aug 2022 17:19:29: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 17:19:29: #1 finished! INFO @ Tue, 02 Aug 2022 17:19:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:19:30: #2 number of paired peaks: 2441 INFO @ Tue, 02 Aug 2022 17:19:30: start model_add_line... INFO @ Tue, 02 Aug 2022 17:19:30: start X-correlation... INFO @ Tue, 02 Aug 2022 17:19:30: end of X-cor INFO @ Tue, 02 Aug 2022 17:19:30: #2 finished! INFO @ Tue, 02 Aug 2022 17:19:30: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 17:19:30: #2 alternative fragment length(s) may be 191 bps INFO @ Tue, 02 Aug 2022 17:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.20_model.r WARNING @ Tue, 02 Aug 2022 17:19:30: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:19:30: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Tue, 02 Aug 2022 17:19:30: #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 17:19:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:19:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:19:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:19:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:19:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:19:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.10_summits.bed INFO @ Tue, 02 Aug 2022 17:19:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4195 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:20:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:20:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:20:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232167/SRX14232167.20_summits.bed INFO @ Tue, 02 Aug 2022 17:20:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3229 records, 4 fields): 45 millis CompletedMACS2peakCalling