Job ID = 16439370 SRX = SRX14232180 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20583413 spots for SRR18080638/SRR18080638.sra Written 20583413 spots for SRR18080638/SRR18080638.sra fastq に変換しました。 bowtie でマッピング中... Your job 16441514 ("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: 04:12:01 20583413 reads; of these: 20583413 (100.00%) were paired; of these: 5360241 (26.04%) aligned concordantly 0 times 8534413 (41.46%) aligned concordantly exactly 1 time 6688759 (32.50%) aligned concordantly >1 times ---- 5360241 pairs aligned concordantly 0 times; of these: 1346510 (25.12%) aligned discordantly 1 time ---- 4013731 pairs aligned 0 times concordantly or discordantly; of these: 8027462 mates make up the pairs; of these: 5077851 (63.26%) aligned 0 times 397702 (4.95%) aligned exactly 1 time 2551909 (31.79%) aligned >1 times 87.67% overall alignment rate Time searching: 04:12:02 Overall time: 04:12:02 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] 3395599 / 16424393 = 0.2067 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 19:33:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.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 19:33:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 19:33:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 19:33:55: 1000000 INFO @ Tue, 02 Aug 2022 19:34:06: 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 19:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.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 19:34:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 19:34:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 19:34:16: 3000000 INFO @ Tue, 02 Aug 2022 19:34:26: 1000000 INFO @ Tue, 02 Aug 2022 19:34:27: 4000000 INFO @ Tue, 02 Aug 2022 19:34:37: 2000000 INFO @ Tue, 02 Aug 2022 19:34:38: 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 19:34:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.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 19:34:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 19:34:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 19:34:48: 3000000 INFO @ Tue, 02 Aug 2022 19:34:49: 6000000 INFO @ Tue, 02 Aug 2022 19:34:55: 1000000 INFO @ Tue, 02 Aug 2022 19:35:00: 4000000 INFO @ Tue, 02 Aug 2022 19:35:00: 7000000 INFO @ Tue, 02 Aug 2022 19:35:04: 2000000 INFO @ Tue, 02 Aug 2022 19:35:11: 5000000 INFO @ Tue, 02 Aug 2022 19:35:13: 8000000 INFO @ Tue, 02 Aug 2022 19:35:14: 3000000 INFO @ Tue, 02 Aug 2022 19:35:23: 4000000 INFO @ Tue, 02 Aug 2022 19:35:24: 6000000 INFO @ Tue, 02 Aug 2022 19:35:25: 9000000 INFO @ Tue, 02 Aug 2022 19:35:33: 5000000 INFO @ Tue, 02 Aug 2022 19:35:38: 7000000 INFO @ Tue, 02 Aug 2022 19:35:39: 10000000 INFO @ Tue, 02 Aug 2022 19:35:43: 6000000 INFO @ Tue, 02 Aug 2022 19:35:51: 8000000 INFO @ Tue, 02 Aug 2022 19:35:52: 11000000 INFO @ Tue, 02 Aug 2022 19:35:53: 7000000 INFO @ Tue, 02 Aug 2022 19:36:03: 8000000 INFO @ Tue, 02 Aug 2022 19:36:03: 9000000 INFO @ Tue, 02 Aug 2022 19:36:05: 12000000 INFO @ Tue, 02 Aug 2022 19:36:12: 9000000 INFO @ Tue, 02 Aug 2022 19:36:16: 10000000 INFO @ Tue, 02 Aug 2022 19:36:17: 13000000 INFO @ Tue, 02 Aug 2022 19:36:21: 10000000 INFO @ Tue, 02 Aug 2022 19:36:29: 11000000 INFO @ Tue, 02 Aug 2022 19:36:29: 14000000 INFO @ Tue, 02 Aug 2022 19:36:30: 11000000 INFO @ Tue, 02 Aug 2022 19:36:39: 12000000 INFO @ Tue, 02 Aug 2022 19:36:41: 12000000 INFO @ Tue, 02 Aug 2022 19:36:42: 15000000 INFO @ Tue, 02 Aug 2022 19:36:49: 13000000 INFO @ Tue, 02 Aug 2022 19:36:54: 13000000 INFO @ Tue, 02 Aug 2022 19:36:55: 16000000 INFO @ Tue, 02 Aug 2022 19:36:58: 14000000 INFO @ Tue, 02 Aug 2022 19:37:06: 14000000 INFO @ Tue, 02 Aug 2022 19:37:07: 17000000 INFO @ Tue, 02 Aug 2022 19:37:07: 15000000 INFO @ Tue, 02 Aug 2022 19:37:18: 16000000 INFO @ Tue, 02 Aug 2022 19:37:18: 15000000 INFO @ Tue, 02 Aug 2022 19:37:19: 18000000 INFO @ Tue, 02 Aug 2022 19:37:27: 17000000 INFO @ Tue, 02 Aug 2022 19:37:30: 16000000 INFO @ Tue, 02 Aug 2022 19:37:31: 19000000 INFO @ Tue, 02 Aug 2022 19:37:36: 18000000 INFO @ Tue, 02 Aug 2022 19:37:43: 17000000 INFO @ Tue, 02 Aug 2022 19:37:43: 20000000 INFO @ Tue, 02 Aug 2022 19:37:45: 19000000 INFO @ Tue, 02 Aug 2022 19:37:54: 20000000 INFO @ Tue, 02 Aug 2022 19:37:54: 18000000 INFO @ Tue, 02 Aug 2022 19:37:55: 21000000 INFO @ Tue, 02 Aug 2022 19:38:03: 21000000 INFO @ Tue, 02 Aug 2022 19:38:06: 19000000 INFO @ Tue, 02 Aug 2022 19:38:06: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 19:38:12: 22000000 INFO @ Tue, 02 Aug 2022 19:38:18: 20000000 INFO @ Tue, 02 Aug 2022 19:38:18: 23000000 INFO @ Tue, 02 Aug 2022 19:38:21: 23000000 INFO @ Tue, 02 Aug 2022 19:38:30: 21000000 INFO @ Tue, 02 Aug 2022 19:38:30: 24000000 INFO @ Tue, 02 Aug 2022 19:38:31: 24000000 INFO @ Tue, 02 Aug 2022 19:38:40: 25000000 INFO @ Tue, 02 Aug 2022 19:38:42: 22000000 INFO @ Tue, 02 Aug 2022 19:38:42: 25000000 INFO @ Tue, 02 Aug 2022 19:38:50: 26000000 INFO @ Tue, 02 Aug 2022 19:38:54: 23000000 INFO @ Tue, 02 Aug 2022 19:38:55: 26000000 INFO @ Tue, 02 Aug 2022 19:38:59: 27000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 19:39:06: 24000000 INFO @ Tue, 02 Aug 2022 19:39:07: 27000000 INFO @ Tue, 02 Aug 2022 19:39:09: 28000000 INFO @ Tue, 02 Aug 2022 19:39:19: 29000000 INFO @ Tue, 02 Aug 2022 19:39:19: 25000000 INFO @ Tue, 02 Aug 2022 19:39:19: 28000000 INFO @ Tue, 02 Aug 2022 19:39:22: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 19:39:22: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 19:39:22: #1 total tags in treatment: 12084579 INFO @ Tue, 02 Aug 2022 19:39:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:39:22: #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 19:39:22: #1 tags after filtering in treatment: 8856545 INFO @ Tue, 02 Aug 2022 19:39:22: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 02 Aug 2022 19:39:22: #1 finished! INFO @ Tue, 02 Aug 2022 19:39:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:39:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:39:23: #2 number of paired peaks: 2599 INFO @ Tue, 02 Aug 2022 19:39:23: start model_add_line... INFO @ Tue, 02 Aug 2022 19:39:23: start X-correlation... INFO @ Tue, 02 Aug 2022 19:39:23: end of X-cor INFO @ Tue, 02 Aug 2022 19:39:23: #2 finished! INFO @ Tue, 02 Aug 2022 19:39:23: #2 predicted fragment length is 190 bps INFO @ Tue, 02 Aug 2022 19:39:23: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 02 Aug 2022 19:39:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.20_model.r WARNING @ Tue, 02 Aug 2022 19:39:23: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:39:23: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Tue, 02 Aug 2022 19:39:23: #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 19:39:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:39:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:39:31: 29000000 INFO @ Tue, 02 Aug 2022 19:39:32: 26000000 INFO @ Tue, 02 Aug 2022 19:39:35: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 19:39:35: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 19:39:35: #1 total tags in treatment: 12084579 INFO @ Tue, 02 Aug 2022 19:39:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:39:35: #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 19:39:35: #1 tags after filtering in treatment: 8856545 INFO @ Tue, 02 Aug 2022 19:39:35: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 02 Aug 2022 19:39:35: #1 finished! INFO @ Tue, 02 Aug 2022 19:39:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:39:36: #2 number of paired peaks: 2599 INFO @ Tue, 02 Aug 2022 19:39:36: start model_add_line... INFO @ Tue, 02 Aug 2022 19:39:36: start X-correlation... INFO @ Tue, 02 Aug 2022 19:39:36: end of X-cor INFO @ Tue, 02 Aug 2022 19:39:36: #2 finished! INFO @ Tue, 02 Aug 2022 19:39:36: #2 predicted fragment length is 190 bps INFO @ Tue, 02 Aug 2022 19:39:36: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 02 Aug 2022 19:39:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.05_model.r WARNING @ Tue, 02 Aug 2022 19:39:36: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:39:36: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Tue, 02 Aug 2022 19:39:36: #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 19:39:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:39:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:39:43: 27000000 INFO @ Tue, 02 Aug 2022 19:39:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.20_peaks.xls INFO @ Tue, 02 Aug 2022 19:39:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:39:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.20_summits.bed INFO @ Tue, 02 Aug 2022 19:39:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3145 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 19:39:55: 28000000 INFO @ Tue, 02 Aug 2022 19:39:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:40:07: 29000000 INFO @ Tue, 02 Aug 2022 19:40:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.05_peaks.xls INFO @ Tue, 02 Aug 2022 19:40:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:40:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.05_summits.bed INFO @ Tue, 02 Aug 2022 19:40:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5384 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 19:40:10: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 19:40:10: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 19:40:10: #1 total tags in treatment: 12084579 INFO @ Tue, 02 Aug 2022 19:40:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:40:10: #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 19:40:10: #1 tags after filtering in treatment: 8856545 INFO @ Tue, 02 Aug 2022 19:40:10: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 02 Aug 2022 19:40:10: #1 finished! INFO @ Tue, 02 Aug 2022 19:40:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:40:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:40:11: #2 number of paired peaks: 2599 INFO @ Tue, 02 Aug 2022 19:40:11: start model_add_line... INFO @ Tue, 02 Aug 2022 19:40:11: start X-correlation... INFO @ Tue, 02 Aug 2022 19:40:12: end of X-cor INFO @ Tue, 02 Aug 2022 19:40:12: #2 finished! INFO @ Tue, 02 Aug 2022 19:40:12: #2 predicted fragment length is 190 bps INFO @ Tue, 02 Aug 2022 19:40:12: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 02 Aug 2022 19:40:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.10_model.r WARNING @ Tue, 02 Aug 2022 19:40:12: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:40:12: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Tue, 02 Aug 2022 19:40:12: #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 19:40:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:40:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:40:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:40:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.10_peaks.xls INFO @ Tue, 02 Aug 2022 19:40:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:40:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232180/SRX14232180.10_summits.bed INFO @ Tue, 02 Aug 2022 19:40:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4002 records, 4 fields): 16 millis CompletedMACS2peakCalling