Job ID = 16439331 SRX = SRX14232169 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21899067 spots for SRR18080649/SRR18080649.sra Written 21899067 spots for SRR18080649/SRR18080649.sra fastq に変換しました。 bowtie でマッピング中... Your job 16441983 ("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: 05:16:13 21899067 reads; of these: 21899067 (100.00%) were paired; of these: 6981841 (31.88%) aligned concordantly 0 times 6414020 (29.29%) aligned concordantly exactly 1 time 8503206 (38.83%) aligned concordantly >1 times ---- 6981841 pairs aligned concordantly 0 times; of these: 1292016 (18.51%) aligned discordantly 1 time ---- 5689825 pairs aligned 0 times concordantly or discordantly; of these: 11379650 mates make up the pairs; of these: 7358551 (64.66%) aligned 0 times 413962 (3.64%) aligned exactly 1 time 3607137 (31.70%) aligned >1 times 83.20% overall alignment rate Time searching: 05:16:13 Overall time: 05:16:13 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] 4907269 / 15982801 = 0.3070 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 20:32:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.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 20:32:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 20:32:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 20:32:33: 1000000 INFO @ Tue, 02 Aug 2022 20:32:41: 2000000 INFO @ Tue, 02 Aug 2022 20:32:49: 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 20:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.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 20:32:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 20:32:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 20:32:58: 4000000 INFO @ Tue, 02 Aug 2022 20:33:06: 1000000 INFO @ Tue, 02 Aug 2022 20:33:09: 5000000 INFO @ Tue, 02 Aug 2022 20:33:19: 2000000 INFO @ Tue, 02 Aug 2022 20:33:21: 6000000 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 20:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.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 20:33:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 20:33:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 20:33:34: 3000000 INFO @ Tue, 02 Aug 2022 20:33:37: 7000000 INFO @ Tue, 02 Aug 2022 20:33:41: 1000000 INFO @ Tue, 02 Aug 2022 20:33:50: 4000000 INFO @ Tue, 02 Aug 2022 20:33:53: 8000000 INFO @ Tue, 02 Aug 2022 20:33:58: 2000000 INFO @ Tue, 02 Aug 2022 20:34:04: 5000000 INFO @ Tue, 02 Aug 2022 20:34:07: 9000000 INFO @ Tue, 02 Aug 2022 20:34:09: 3000000 INFO @ Tue, 02 Aug 2022 20:34:14: 6000000 INFO @ Tue, 02 Aug 2022 20:34:19: 10000000 INFO @ Tue, 02 Aug 2022 20:34:21: 4000000 INFO @ Tue, 02 Aug 2022 20:34:28: 7000000 INFO @ Tue, 02 Aug 2022 20:34:34: 5000000 INFO @ Tue, 02 Aug 2022 20:34:35: 11000000 INFO @ Tue, 02 Aug 2022 20:34:40: 8000000 INFO @ Tue, 02 Aug 2022 20:34:46: 6000000 INFO @ Tue, 02 Aug 2022 20:34:46: 12000000 INFO @ Tue, 02 Aug 2022 20:34:51: 9000000 INFO @ Tue, 02 Aug 2022 20:34:56: 7000000 INFO @ Tue, 02 Aug 2022 20:34:57: 13000000 INFO @ Tue, 02 Aug 2022 20:35:01: 10000000 INFO @ Tue, 02 Aug 2022 20:35:07: 8000000 INFO @ Tue, 02 Aug 2022 20:35:07: 14000000 INFO @ Tue, 02 Aug 2022 20:35:12: 11000000 INFO @ Tue, 02 Aug 2022 20:35:17: 9000000 INFO @ Tue, 02 Aug 2022 20:35:18: 15000000 INFO @ Tue, 02 Aug 2022 20:35:23: 12000000 INFO @ Tue, 02 Aug 2022 20:35:31: 10000000 INFO @ Tue, 02 Aug 2022 20:35:31: 16000000 INFO @ Tue, 02 Aug 2022 20:35:37: 13000000 INFO @ Tue, 02 Aug 2022 20:35:48: 11000000 INFO @ Tue, 02 Aug 2022 20:35:48: 17000000 INFO @ Tue, 02 Aug 2022 20:35:52: 14000000 INFO @ Tue, 02 Aug 2022 20:36:04: 12000000 INFO @ Tue, 02 Aug 2022 20:36:05: 18000000 INFO @ Tue, 02 Aug 2022 20:36:07: 15000000 INFO @ Tue, 02 Aug 2022 20:36:18: 19000000 INFO @ Tue, 02 Aug 2022 20:36:18: 13000000 INFO @ Tue, 02 Aug 2022 20:36:19: 16000000 INFO @ Tue, 02 Aug 2022 20:36:32: 20000000 INFO @ Tue, 02 Aug 2022 20:36:35: 17000000 INFO @ Tue, 02 Aug 2022 20:36:35: 14000000 INFO @ Tue, 02 Aug 2022 20:36:43: 21000000 INFO @ Tue, 02 Aug 2022 20:36:45: 18000000 INFO @ Tue, 02 Aug 2022 20:36:46: 15000000 INFO @ Tue, 02 Aug 2022 20:36:57: 22000000 INFO @ Tue, 02 Aug 2022 20:36:58: 19000000 INFO @ Tue, 02 Aug 2022 20:37:01: 16000000 INFO @ Tue, 02 Aug 2022 20:37:09: 23000000 INFO @ Tue, 02 Aug 2022 20:37:10: 20000000 INFO @ Tue, 02 Aug 2022 20:37:12: 17000000 INFO @ Tue, 02 Aug 2022 20:37:20: 24000000 INFO @ Tue, 02 Aug 2022 20:37:20: 21000000 INFO @ Tue, 02 Aug 2022 20:37:22: 18000000 INFO @ Tue, 02 Aug 2022 20:37:30: 22000000 INFO @ Tue, 02 Aug 2022 20:37:30: 25000000 INFO @ Tue, 02 Aug 2022 20:37:32: 19000000 INFO @ Tue, 02 Aug 2022 20:37:40: 23000000 INFO @ Tue, 02 Aug 2022 20:37:41: 26000000 INFO @ Tue, 02 Aug 2022 20:37:42: 20000000 INFO @ Tue, 02 Aug 2022 20:37:48: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 20:37:48: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 20:37:48: #1 total tags in treatment: 10303175 INFO @ Tue, 02 Aug 2022 20:37:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 20:37:48: #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 20:37:48: #1 tags after filtering in treatment: 6957270 INFO @ Tue, 02 Aug 2022 20:37:48: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 02 Aug 2022 20:37:48: #1 finished! INFO @ Tue, 02 Aug 2022 20:37:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 20:37:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 20:37:49: #2 number of paired peaks: 2964 INFO @ Tue, 02 Aug 2022 20:37:49: start model_add_line... INFO @ Tue, 02 Aug 2022 20:37:49: start X-correlation... INFO @ Tue, 02 Aug 2022 20:37:49: end of X-cor INFO @ Tue, 02 Aug 2022 20:37:49: #2 finished! INFO @ Tue, 02 Aug 2022 20:37:49: #2 predicted fragment length is 180 bps INFO @ Tue, 02 Aug 2022 20:37:49: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 02 Aug 2022 20:37:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.05_model.r WARNING @ Tue, 02 Aug 2022 20:37:49: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 20:37:49: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Tue, 02 Aug 2022 20:37:49: #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 20:37:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 20:37:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 20:37:50: 24000000 INFO @ Tue, 02 Aug 2022 20:37:51: 21000000 INFO @ Tue, 02 Aug 2022 20:38:00: 25000000 INFO @ Tue, 02 Aug 2022 20:38:01: 22000000 INFO @ Tue, 02 Aug 2022 20:38:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 20:38:10: 23000000 INFO @ Tue, 02 Aug 2022 20:38:10: 26000000 INFO @ Tue, 02 Aug 2022 20:38:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.05_peaks.xls INFO @ Tue, 02 Aug 2022 20:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 20:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.05_summits.bed INFO @ Tue, 02 Aug 2022 20:38:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4854 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 20:38:17: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 20:38:17: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 20:38:17: #1 total tags in treatment: 10303175 INFO @ Tue, 02 Aug 2022 20:38:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 20:38:17: #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 20:38:17: #1 tags after filtering in treatment: 6957270 INFO @ Tue, 02 Aug 2022 20:38:17: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 02 Aug 2022 20:38:17: #1 finished! INFO @ Tue, 02 Aug 2022 20:38:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 20:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 20:38:18: #2 number of paired peaks: 2964 INFO @ Tue, 02 Aug 2022 20:38:18: start model_add_line... INFO @ Tue, 02 Aug 2022 20:38:18: start X-correlation... INFO @ Tue, 02 Aug 2022 20:38:18: end of X-cor INFO @ Tue, 02 Aug 2022 20:38:18: #2 finished! INFO @ Tue, 02 Aug 2022 20:38:18: #2 predicted fragment length is 180 bps INFO @ Tue, 02 Aug 2022 20:38:18: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 02 Aug 2022 20:38:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.10_model.r WARNING @ Tue, 02 Aug 2022 20:38:18: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 20:38:18: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Tue, 02 Aug 2022 20:38:18: #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 20:38:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 20:38:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 20:38:20: 24000000 INFO @ Tue, 02 Aug 2022 20:38:28: 25000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 20:38:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 20:38:37: 26000000 INFO @ Tue, 02 Aug 2022 20:38:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.10_peaks.xls INFO @ Tue, 02 Aug 2022 20:38:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 20:38:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.10_summits.bed INFO @ Tue, 02 Aug 2022 20:38:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3831 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 20:38:43: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 20:38:43: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 20:38:43: #1 total tags in treatment: 10303175 INFO @ Tue, 02 Aug 2022 20:38:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 20:38:43: #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 20:38:43: #1 tags after filtering in treatment: 6957270 INFO @ Tue, 02 Aug 2022 20:38:43: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 02 Aug 2022 20:38:43: #1 finished! INFO @ Tue, 02 Aug 2022 20:38:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 20:38:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 20:38:44: #2 number of paired peaks: 2964 INFO @ Tue, 02 Aug 2022 20:38:44: start model_add_line... INFO @ Tue, 02 Aug 2022 20:38:44: start X-correlation... INFO @ Tue, 02 Aug 2022 20:38:44: end of X-cor INFO @ Tue, 02 Aug 2022 20:38:44: #2 finished! INFO @ Tue, 02 Aug 2022 20:38:44: #2 predicted fragment length is 180 bps INFO @ Tue, 02 Aug 2022 20:38:44: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 02 Aug 2022 20:38:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.20_model.r WARNING @ Tue, 02 Aug 2022 20:38:44: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 20:38:44: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Tue, 02 Aug 2022 20:38:44: #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 20:38:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 20:38:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 20:39:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 20:39:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.20_peaks.xls INFO @ Tue, 02 Aug 2022 20:39:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 20:39:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232169/SRX14232169.20_summits.bed INFO @ Tue, 02 Aug 2022 20:39:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3161 records, 4 fields): 6 millis CompletedMACS2peakCalling