Job ID = 14167146 SRX = SRX10340455 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 972376 READS because READLEN < 1 Read 14697377 spots for SRR13962464/SRR13962464.sra Written 14697377 spots for SRR13962464/SRR13962464.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167722 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) 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 16 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] 1 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 1 unmatched pairs [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] 1 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2418771 / 12312880 = 0.1964 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted 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 11:06:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.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 11:06:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:06:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:07:02: 1000000 INFO @ Fri, 10 Dec 2021 11:07:10: 2000000 INFO @ Fri, 10 Dec 2021 11:07:17: 3000000 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 11:07:24: 4000000 INFO @ Fri, 10 Dec 2021 11:07:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.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 11:07:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:07:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:07:33: 5000000 INFO @ Fri, 10 Dec 2021 11:07:34: 1000000 INFO @ Fri, 10 Dec 2021 11:07:42: 6000000 INFO @ Fri, 10 Dec 2021 11:07:43: 2000000 INFO @ Fri, 10 Dec 2021 11:07:51: 7000000 INFO @ Fri, 10 Dec 2021 11:07:52: 3000000 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 11:07:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.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 11:07:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:07:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:08:00: 8000000 INFO @ Fri, 10 Dec 2021 11:08:01: 4000000 INFO @ Fri, 10 Dec 2021 11:08:04: 1000000 INFO @ Fri, 10 Dec 2021 11:08:09: 9000000 INFO @ Fri, 10 Dec 2021 11:08:10: 5000000 INFO @ Fri, 10 Dec 2021 11:08:13: 2000000 INFO @ Fri, 10 Dec 2021 11:08:18: 10000000 INFO @ Fri, 10 Dec 2021 11:08:19: 6000000 INFO @ Fri, 10 Dec 2021 11:08:22: 3000000 INFO @ Fri, 10 Dec 2021 11:08:28: 11000000 INFO @ Fri, 10 Dec 2021 11:08:28: 7000000 INFO @ Fri, 10 Dec 2021 11:08:31: 4000000 INFO @ Fri, 10 Dec 2021 11:08:37: 12000000 INFO @ Fri, 10 Dec 2021 11:08:38: 8000000 INFO @ Fri, 10 Dec 2021 11:08:41: 5000000 INFO @ Fri, 10 Dec 2021 11:08:46: 13000000 INFO @ Fri, 10 Dec 2021 11:08:47: 9000000 INFO @ Fri, 10 Dec 2021 11:08:50: 6000000 INFO @ Fri, 10 Dec 2021 11:08:55: 14000000 INFO @ Fri, 10 Dec 2021 11:08:56: 10000000 INFO @ Fri, 10 Dec 2021 11:08:59: 7000000 INFO @ Fri, 10 Dec 2021 11:09:04: 15000000 INFO @ Fri, 10 Dec 2021 11:09:05: 11000000 INFO @ Fri, 10 Dec 2021 11:09:08: 8000000 INFO @ Fri, 10 Dec 2021 11:09:13: 16000000 INFO @ Fri, 10 Dec 2021 11:09:14: 12000000 INFO @ Fri, 10 Dec 2021 11:09:17: 9000000 INFO @ Fri, 10 Dec 2021 11:09:23: 17000000 INFO @ Fri, 10 Dec 2021 11:09:23: 13000000 INFO @ Fri, 10 Dec 2021 11:09:26: 10000000 INFO @ Fri, 10 Dec 2021 11:09:32: 18000000 INFO @ Fri, 10 Dec 2021 11:09:32: 14000000 INFO @ Fri, 10 Dec 2021 11:09:35: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:09:41: 19000000 INFO @ Fri, 10 Dec 2021 11:09:41: 15000000 INFO @ Fri, 10 Dec 2021 11:09:44: 12000000 INFO @ Fri, 10 Dec 2021 11:09:50: 20000000 INFO @ Fri, 10 Dec 2021 11:09:50: 16000000 INFO @ Fri, 10 Dec 2021 11:09:53: 13000000 INFO @ Fri, 10 Dec 2021 11:09:57: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:09:57: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:09:57: #1 total tags in treatment: 9811406 INFO @ Fri, 10 Dec 2021 11:09:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:09:57: #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 11:09:58: #1 tags after filtering in treatment: 9054339 INFO @ Fri, 10 Dec 2021 11:09:58: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 11:09:58: #1 finished! INFO @ Fri, 10 Dec 2021 11:09:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:09:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:09:58: #2 number of paired peaks: 4058 INFO @ Fri, 10 Dec 2021 11:09:59: start model_add_line... INFO @ Fri, 10 Dec 2021 11:09:59: start X-correlation... INFO @ Fri, 10 Dec 2021 11:09:59: end of X-cor INFO @ Fri, 10 Dec 2021 11:09:59: #2 finished! INFO @ Fri, 10 Dec 2021 11:09:59: #2 predicted fragment length is 242 bps INFO @ Fri, 10 Dec 2021 11:09:59: #2 alternative fragment length(s) may be 242 bps INFO @ Fri, 10 Dec 2021 11:09:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.05_model.r WARNING @ Fri, 10 Dec 2021 11:09:59: #2 Since the d (242) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:09:59: #2 You may need to consider one of the other alternative d(s): 242 WARNING @ Fri, 10 Dec 2021 11:09:59: #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 11:09:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:09:59: 17000000 INFO @ Fri, 10 Dec 2021 11:10:02: 14000000 INFO @ Fri, 10 Dec 2021 11:10:08: 18000000 INFO @ Fri, 10 Dec 2021 11:10:11: 15000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:10:17: 19000000 INFO @ Fri, 10 Dec 2021 11:10:20: 16000000 INFO @ Fri, 10 Dec 2021 11:10:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:10:26: 20000000 INFO @ Fri, 10 Dec 2021 11:10:29: 17000000 INFO @ Fri, 10 Dec 2021 11:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.05_summits.bed INFO @ Fri, 10 Dec 2021 11:10:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7988 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:10:34: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:10:34: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:10:34: #1 total tags in treatment: 9811406 INFO @ Fri, 10 Dec 2021 11:10:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:10:34: #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 11:10:34: #1 tags after filtering in treatment: 9054339 INFO @ Fri, 10 Dec 2021 11:10:34: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 11:10:34: #1 finished! INFO @ Fri, 10 Dec 2021 11:10:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:10:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:10:35: #2 number of paired peaks: 4058 INFO @ Fri, 10 Dec 2021 11:10:35: start model_add_line... INFO @ Fri, 10 Dec 2021 11:10:35: start X-correlation... INFO @ Fri, 10 Dec 2021 11:10:35: end of X-cor INFO @ Fri, 10 Dec 2021 11:10:35: #2 finished! INFO @ Fri, 10 Dec 2021 11:10:35: #2 predicted fragment length is 242 bps INFO @ Fri, 10 Dec 2021 11:10:35: #2 alternative fragment length(s) may be 242 bps INFO @ Fri, 10 Dec 2021 11:10:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.10_model.r WARNING @ Fri, 10 Dec 2021 11:10:35: #2 Since the d (242) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:10:35: #2 You may need to consider one of the other alternative d(s): 242 WARNING @ Fri, 10 Dec 2021 11:10:35: #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 11:10:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:10:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:10:38: 18000000 INFO @ Fri, 10 Dec 2021 11:10:46: 19000000 INFO @ Fri, 10 Dec 2021 11:10:54: 20000000 INFO @ Fri, 10 Dec 2021 11:10:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:11:01: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:11:01: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:11:01: #1 total tags in treatment: 9811406 INFO @ Fri, 10 Dec 2021 11:11:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:11:01: #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 11:11:01: #1 tags after filtering in treatment: 9054339 INFO @ Fri, 10 Dec 2021 11:11:01: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 11:11:01: #1 finished! INFO @ Fri, 10 Dec 2021 11:11:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:11:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:11:02: #2 number of paired peaks: 4058 INFO @ Fri, 10 Dec 2021 11:11:02: start model_add_line... INFO @ Fri, 10 Dec 2021 11:11:02: start X-correlation... INFO @ Fri, 10 Dec 2021 11:11:02: end of X-cor INFO @ Fri, 10 Dec 2021 11:11:02: #2 finished! INFO @ Fri, 10 Dec 2021 11:11:02: #2 predicted fragment length is 242 bps INFO @ Fri, 10 Dec 2021 11:11:02: #2 alternative fragment length(s) may be 242 bps INFO @ Fri, 10 Dec 2021 11:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.20_model.r WARNING @ Fri, 10 Dec 2021 11:11:02: #2 Since the d (242) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:11:02: #2 You may need to consider one of the other alternative d(s): 242 WARNING @ Fri, 10 Dec 2021 11:11:02: #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 11:11:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.10_summits.bed INFO @ Fri, 10 Dec 2021 11:11:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6704 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:11:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:11:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:11:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:11:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340455/SRX10340455.20_summits.bed INFO @ Fri, 10 Dec 2021 11:11:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5022 records, 4 fields): 6 millis CompletedMACS2peakCalling