Job ID = 14168314 SRX = SRX9263549 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30042585 spots for SRR12794429/SRR12794429.sra Written 30042585 spots for SRR12794429/SRR12794429.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169659 ("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: 01:44:49 30042585 reads; of these: 30042585 (100.00%) were paired; of these: 15241424 (50.73%) aligned concordantly 0 times 9288146 (30.92%) aligned concordantly exactly 1 time 5513015 (18.35%) aligned concordantly >1 times ---- 15241424 pairs aligned concordantly 0 times; of these: 3332441 (21.86%) aligned discordantly 1 time ---- 11908983 pairs aligned 0 times concordantly or discordantly; of these: 23817966 mates make up the pairs; of these: 18978989 (79.68%) aligned 0 times 1047303 (4.40%) aligned exactly 1 time 3791674 (15.92%) aligned >1 times 68.41% overall alignment rate Time searching: 01:44:49 Overall time: 01:44:49 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 32 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] 5095387 / 18025909 = 0.2827 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 19:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.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 @ Fri, 10 Dec 2021 19:28:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:28:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:29:07: 1000000 INFO @ Fri, 10 Dec 2021 19:29:17: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 19:29:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.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 @ Fri, 10 Dec 2021 19:29:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:29:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:29:28: 3000000 INFO @ Fri, 10 Dec 2021 19:29:39: 4000000 INFO @ Fri, 10 Dec 2021 19:29:40: 1000000 INFO @ Fri, 10 Dec 2021 19:29:50: 5000000 INFO @ Fri, 10 Dec 2021 19:29:53: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 19:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.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 @ Fri, 10 Dec 2021 19:29:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:29:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:30:01: 6000000 INFO @ Fri, 10 Dec 2021 19:30:07: 3000000 INFO @ Fri, 10 Dec 2021 19:30:07: 1000000 INFO @ Fri, 10 Dec 2021 19:30:13: 7000000 INFO @ Fri, 10 Dec 2021 19:30:18: 2000000 INFO @ Fri, 10 Dec 2021 19:30:20: 4000000 INFO @ Fri, 10 Dec 2021 19:30:24: 8000000 INFO @ Fri, 10 Dec 2021 19:30:29: 3000000 INFO @ Fri, 10 Dec 2021 19:30:34: 5000000 INFO @ Fri, 10 Dec 2021 19:30:35: 9000000 INFO @ Fri, 10 Dec 2021 19:30:41: 4000000 INFO @ Fri, 10 Dec 2021 19:30:47: 10000000 INFO @ Fri, 10 Dec 2021 19:30:47: 6000000 INFO @ Fri, 10 Dec 2021 19:30:52: 5000000 INFO @ Fri, 10 Dec 2021 19:30:58: 11000000 INFO @ Fri, 10 Dec 2021 19:31:01: 7000000 INFO @ Fri, 10 Dec 2021 19:31:04: 6000000 INFO @ Fri, 10 Dec 2021 19:31:10: 12000000 INFO @ Fri, 10 Dec 2021 19:31:14: 8000000 INFO @ Fri, 10 Dec 2021 19:31:15: 7000000 INFO @ Fri, 10 Dec 2021 19:31:21: 13000000 INFO @ Fri, 10 Dec 2021 19:31:26: 8000000 INFO @ Fri, 10 Dec 2021 19:31:28: 9000000 INFO @ Fri, 10 Dec 2021 19:31:32: 14000000 INFO @ Fri, 10 Dec 2021 19:31:37: 9000000 INFO @ Fri, 10 Dec 2021 19:31:41: 10000000 INFO @ Fri, 10 Dec 2021 19:31:44: 15000000 INFO @ Fri, 10 Dec 2021 19:31:49: 10000000 INFO @ Fri, 10 Dec 2021 19:31:54: 11000000 INFO @ Fri, 10 Dec 2021 19:31:55: 16000000 INFO @ Fri, 10 Dec 2021 19:32:00: 11000000 INFO @ Fri, 10 Dec 2021 19:32:06: 17000000 INFO @ Fri, 10 Dec 2021 19:32:08: 12000000 INFO @ Fri, 10 Dec 2021 19:32:11: 12000000 INFO @ Fri, 10 Dec 2021 19:32:17: 18000000 INFO @ Fri, 10 Dec 2021 19:32:21: 13000000 INFO @ Fri, 10 Dec 2021 19:32:22: 13000000 INFO @ Fri, 10 Dec 2021 19:32:28: 19000000 INFO @ Fri, 10 Dec 2021 19:32:34: 14000000 INFO @ Fri, 10 Dec 2021 19:32:35: 14000000 INFO @ Fri, 10 Dec 2021 19:32:39: 20000000 INFO @ Fri, 10 Dec 2021 19:32:45: 15000000 INFO @ Fri, 10 Dec 2021 19:32:49: 15000000 INFO @ Fri, 10 Dec 2021 19:32:50: 21000000 INFO @ Fri, 10 Dec 2021 19:32:56: 16000000 INFO @ Fri, 10 Dec 2021 19:33:01: 22000000 INFO @ Fri, 10 Dec 2021 19:33:03: 16000000 INFO @ Fri, 10 Dec 2021 19:33:07: 17000000 INFO @ Fri, 10 Dec 2021 19:33:12: 23000000 INFO @ Fri, 10 Dec 2021 19:33:16: 17000000 INFO @ Fri, 10 Dec 2021 19:33:18: 18000000 INFO @ Fri, 10 Dec 2021 19:33:23: 24000000 INFO @ Fri, 10 Dec 2021 19:33:29: 18000000 INFO @ Fri, 10 Dec 2021 19:33:29: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:33:34: 25000000 INFO @ Fri, 10 Dec 2021 19:33:40: 20000000 INFO @ Fri, 10 Dec 2021 19:33:42: 19000000 INFO @ Fri, 10 Dec 2021 19:33:46: 26000000 INFO @ Fri, 10 Dec 2021 19:33:51: 21000000 INFO @ Fri, 10 Dec 2021 19:33:55: 20000000 INFO @ Fri, 10 Dec 2021 19:33:57: 27000000 INFO @ Fri, 10 Dec 2021 19:34:02: 22000000 INFO @ Fri, 10 Dec 2021 19:34:08: 21000000 INFO @ Fri, 10 Dec 2021 19:34:08: 28000000 INFO @ Fri, 10 Dec 2021 19:34:13: 23000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:34:20: 29000000 INFO @ Fri, 10 Dec 2021 19:34:21: 22000000 INFO @ Fri, 10 Dec 2021 19:34:24: 24000000 INFO @ Fri, 10 Dec 2021 19:34:31: 30000000 INFO @ Fri, 10 Dec 2021 19:34:34: 23000000 INFO @ Fri, 10 Dec 2021 19:34:35: 25000000 INFO @ Fri, 10 Dec 2021 19:34:41: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 19:34:41: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 19:34:41: #1 total tags in treatment: 10161957 INFO @ Fri, 10 Dec 2021 19:34:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:34:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 19:34:41: #1 tags after filtering in treatment: 6655308 INFO @ Fri, 10 Dec 2021 19:34:41: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 10 Dec 2021 19:34:41: #1 finished! INFO @ Fri, 10 Dec 2021 19:34:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:34:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:34:42: #2 number of paired peaks: 4196 INFO @ Fri, 10 Dec 2021 19:34:42: start model_add_line... INFO @ Fri, 10 Dec 2021 19:34:42: start X-correlation... INFO @ Fri, 10 Dec 2021 19:34:42: end of X-cor INFO @ Fri, 10 Dec 2021 19:34:42: #2 finished! INFO @ Fri, 10 Dec 2021 19:34:42: #2 predicted fragment length is 197 bps INFO @ Fri, 10 Dec 2021 19:34:42: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 10 Dec 2021 19:34:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.05_model.r WARNING @ Fri, 10 Dec 2021 19:34:42: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:34:42: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 10 Dec 2021 19:34:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 19:34:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:34:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:34:46: 26000000 INFO @ Fri, 10 Dec 2021 19:34:48: 24000000 INFO @ Fri, 10 Dec 2021 19:34:57: 27000000 INFO @ Fri, 10 Dec 2021 19:35:01: 25000000 INFO @ Fri, 10 Dec 2021 19:35:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:35:08: 28000000 INFO @ Fri, 10 Dec 2021 19:35:15: 26000000 INFO @ Fri, 10 Dec 2021 19:35:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:35:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:35:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.05_summits.bed INFO @ Fri, 10 Dec 2021 19:35:17: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9565 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:35:19: 29000000 INFO @ Fri, 10 Dec 2021 19:35:29: 27000000 INFO @ Fri, 10 Dec 2021 19:35:31: 30000000 INFO @ Fri, 10 Dec 2021 19:35:40: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 19:35:40: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 19:35:40: #1 total tags in treatment: 10161957 INFO @ Fri, 10 Dec 2021 19:35:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:35:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 19:35:41: #1 tags after filtering in treatment: 6655308 INFO @ Fri, 10 Dec 2021 19:35:41: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 10 Dec 2021 19:35:41: #1 finished! INFO @ Fri, 10 Dec 2021 19:35:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:35:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:35:42: #2 number of paired peaks: 4196 INFO @ Fri, 10 Dec 2021 19:35:42: start model_add_line... INFO @ Fri, 10 Dec 2021 19:35:42: start X-correlation... INFO @ Fri, 10 Dec 2021 19:35:42: end of X-cor INFO @ Fri, 10 Dec 2021 19:35:42: #2 finished! INFO @ Fri, 10 Dec 2021 19:35:42: #2 predicted fragment length is 197 bps INFO @ Fri, 10 Dec 2021 19:35:42: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 10 Dec 2021 19:35:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.20_model.r WARNING @ Fri, 10 Dec 2021 19:35:42: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:35:42: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 10 Dec 2021 19:35:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 19:35:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:35:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:35:42: 28000000 INFO @ Fri, 10 Dec 2021 19:35:55: 29000000 INFO @ Fri, 10 Dec 2021 19:36:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:36:08: 30000000 INFO @ Fri, 10 Dec 2021 19:36:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:36:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:36:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.20_summits.bed INFO @ Fri, 10 Dec 2021 19:36:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2676 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:36:20: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 19:36:20: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 19:36:20: #1 total tags in treatment: 10161957 INFO @ Fri, 10 Dec 2021 19:36:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:36:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 19:36:20: #1 tags after filtering in treatment: 6655308 INFO @ Fri, 10 Dec 2021 19:36:20: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 10 Dec 2021 19:36:20: #1 finished! INFO @ Fri, 10 Dec 2021 19:36:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:36:21: #2 number of paired peaks: 4196 INFO @ Fri, 10 Dec 2021 19:36:21: start model_add_line... INFO @ Fri, 10 Dec 2021 19:36:21: start X-correlation... INFO @ Fri, 10 Dec 2021 19:36:21: end of X-cor INFO @ Fri, 10 Dec 2021 19:36:21: #2 finished! INFO @ Fri, 10 Dec 2021 19:36:21: #2 predicted fragment length is 197 bps INFO @ Fri, 10 Dec 2021 19:36:21: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 10 Dec 2021 19:36:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.10_model.r WARNING @ Fri, 10 Dec 2021 19:36:21: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:36:21: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 10 Dec 2021 19:36:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 19:36:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:36:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:36:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:36:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:36:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:36:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263549/SRX9263549.10_summits.bed INFO @ Fri, 10 Dec 2021 19:36:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5999 records, 4 fields): 9 millis CompletedMACS2peakCalling