Job ID = 14171306 SRX = SRX9005669 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 751596 READS because READLEN < 1 Read 10589624 spots for SRR12515070/SRR12515070.sra Written 10589624 spots for SRR12515070/SRR12515070.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171824 ("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 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 3 unmatched pairs [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] 1 unmatched pairs [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] 3 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1838159 / 8914596 = 0.2062 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 @ Sat, 11 Dec 2021 11:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.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 @ Sat, 11 Dec 2021 11:36:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:36:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:36:50: 1000000 INFO @ Sat, 11 Dec 2021 11:36:57: 2000000 INFO @ Sat, 11 Dec 2021 11:37:04: 3000000 INFO @ Sat, 11 Dec 2021 11:37:10: 4000000 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 @ Sat, 11 Dec 2021 11:37:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.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 @ Sat, 11 Dec 2021 11:37:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:37:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:37:18: 5000000 INFO @ Sat, 11 Dec 2021 11:37:20: 1000000 INFO @ Sat, 11 Dec 2021 11:37:25: 6000000 INFO @ Sat, 11 Dec 2021 11:37:28: 2000000 INFO @ Sat, 11 Dec 2021 11:37:33: 7000000 INFO @ Sat, 11 Dec 2021 11:37:35: 3000000 INFO @ Sat, 11 Dec 2021 11:37:40: 8000000 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 @ Sat, 11 Dec 2021 11:37:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.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 @ Sat, 11 Dec 2021 11:37:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:37:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:37:43: 4000000 INFO @ Sat, 11 Dec 2021 11:37:48: 9000000 INFO @ Sat, 11 Dec 2021 11:37:51: 5000000 INFO @ Sat, 11 Dec 2021 11:37:51: 1000000 INFO @ Sat, 11 Dec 2021 11:37:56: 10000000 INFO @ Sat, 11 Dec 2021 11:37:58: 6000000 INFO @ Sat, 11 Dec 2021 11:38:00: 2000000 INFO @ Sat, 11 Dec 2021 11:38:04: 11000000 INFO @ Sat, 11 Dec 2021 11:38:06: 7000000 INFO @ Sat, 11 Dec 2021 11:38:10: 3000000 INFO @ Sat, 11 Dec 2021 11:38:12: 12000000 INFO @ Sat, 11 Dec 2021 11:38:15: 8000000 INFO @ Sat, 11 Dec 2021 11:38:19: 4000000 INFO @ Sat, 11 Dec 2021 11:38:20: 13000000 INFO @ Sat, 11 Dec 2021 11:38:23: 9000000 INFO @ Sat, 11 Dec 2021 11:38:28: 5000000 INFO @ Sat, 11 Dec 2021 11:38:28: 14000000 INFO @ Sat, 11 Dec 2021 11:38:31: 10000000 INFO @ Sat, 11 Dec 2021 11:38:36: 15000000 INFO @ Sat, 11 Dec 2021 11:38:37: 6000000 INFO @ Sat, 11 Dec 2021 11:38:38: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:38:38: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:38:38: #1 total tags in treatment: 6923592 INFO @ Sat, 11 Dec 2021 11:38:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:38:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:38:38: #1 tags after filtering in treatment: 5600741 INFO @ Sat, 11 Dec 2021 11:38:38: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 11 Dec 2021 11:38:38: #1 finished! INFO @ Sat, 11 Dec 2021 11:38:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:38:39: #2 number of paired peaks: 7005 INFO @ Sat, 11 Dec 2021 11:38:39: start model_add_line... INFO @ Sat, 11 Dec 2021 11:38:39: start X-correlation... INFO @ Sat, 11 Dec 2021 11:38:39: end of X-cor INFO @ Sat, 11 Dec 2021 11:38:39: #2 finished! INFO @ Sat, 11 Dec 2021 11:38:39: #2 predicted fragment length is 227 bps INFO @ Sat, 11 Dec 2021 11:38:39: #2 alternative fragment length(s) may be 227 bps INFO @ Sat, 11 Dec 2021 11:38:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.05_model.r WARNING @ Sat, 11 Dec 2021 11:38:39: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:38:39: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Sat, 11 Dec 2021 11:38:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:38:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:38:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:38:39: 11000000 INFO @ Sat, 11 Dec 2021 11:38:46: 7000000 INFO @ Sat, 11 Dec 2021 11:38:46: 12000000 INFO @ Sat, 11 Dec 2021 11:38:54: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:38:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:38:55: 8000000 INFO @ Sat, 11 Dec 2021 11:39:02: 14000000 INFO @ Sat, 11 Dec 2021 11:39:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:39:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:39:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.05_summits.bed INFO @ Sat, 11 Dec 2021 11:39:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7863 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:39:04: 9000000 INFO @ Sat, 11 Dec 2021 11:39:10: 15000000 INFO @ Sat, 11 Dec 2021 11:39:11: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:39:11: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:39:11: #1 total tags in treatment: 6923592 INFO @ Sat, 11 Dec 2021 11:39:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:39:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:39:11: #1 tags after filtering in treatment: 5600741 INFO @ Sat, 11 Dec 2021 11:39:11: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 11 Dec 2021 11:39:11: #1 finished! INFO @ Sat, 11 Dec 2021 11:39:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:39:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:39:12: #2 number of paired peaks: 7005 INFO @ Sat, 11 Dec 2021 11:39:12: start model_add_line... INFO @ Sat, 11 Dec 2021 11:39:12: start X-correlation... INFO @ Sat, 11 Dec 2021 11:39:12: end of X-cor INFO @ Sat, 11 Dec 2021 11:39:12: #2 finished! INFO @ Sat, 11 Dec 2021 11:39:12: #2 predicted fragment length is 227 bps INFO @ Sat, 11 Dec 2021 11:39:12: #2 alternative fragment length(s) may be 227 bps INFO @ Sat, 11 Dec 2021 11:39:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.10_model.r WARNING @ Sat, 11 Dec 2021 11:39:12: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:39:12: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Sat, 11 Dec 2021 11:39:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:39:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:39:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:39:13: 10000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:39:22: 11000000 INFO @ Sat, 11 Dec 2021 11:39:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:39:30: 12000000 INFO @ Sat, 11 Dec 2021 11:39:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:39:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:39:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.10_summits.bed INFO @ Sat, 11 Dec 2021 11:39:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6339 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:39:39: 13000000 INFO @ Sat, 11 Dec 2021 11:39:48: 14000000 INFO @ Sat, 11 Dec 2021 11:39:56: 15000000 INFO @ Sat, 11 Dec 2021 11:39:58: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:39:58: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:39:58: #1 total tags in treatment: 6923592 INFO @ Sat, 11 Dec 2021 11:39:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:39:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:39:58: #1 tags after filtering in treatment: 5600741 INFO @ Sat, 11 Dec 2021 11:39:58: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 11 Dec 2021 11:39:58: #1 finished! INFO @ Sat, 11 Dec 2021 11:39:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:39:59: #2 number of paired peaks: 7005 INFO @ Sat, 11 Dec 2021 11:39:59: start model_add_line... INFO @ Sat, 11 Dec 2021 11:39:59: start X-correlation... INFO @ Sat, 11 Dec 2021 11:39:59: end of X-cor INFO @ Sat, 11 Dec 2021 11:39:59: #2 finished! INFO @ Sat, 11 Dec 2021 11:39:59: #2 predicted fragment length is 227 bps INFO @ Sat, 11 Dec 2021 11:39:59: #2 alternative fragment length(s) may be 227 bps INFO @ Sat, 11 Dec 2021 11:39:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.20_model.r WARNING @ Sat, 11 Dec 2021 11:39:59: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:39:59: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Sat, 11 Dec 2021 11:39:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:39:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:39:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:40:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:40:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:40:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:40:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005669/SRX9005669.20_summits.bed INFO @ Sat, 11 Dec 2021 11:40:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4606 records, 4 fields): 6 millis CompletedMACS2peakCalling