Job ID = 14171302 SRX = SRX9005665 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1152173 READS because READLEN < 1 Read 11122704 spots for SRR12515066/SRR12515066.sra Written 11122704 spots for SRR12515066/SRR12515066.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171890 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 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] 1 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 2 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] 3 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1862686 / 8734869 = 0.2132 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 11:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.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 11:49:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:49:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:50:01: 1000000 INFO @ Sat, 11 Dec 2021 11:50:12: 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 @ Sat, 11 Dec 2021 11:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.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 11:50:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:50:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:50:24: 3000000 INFO @ Sat, 11 Dec 2021 11:50:33: 1000000 INFO @ Sat, 11 Dec 2021 11:50:35: 4000000 INFO @ Sat, 11 Dec 2021 11:50:45: 2000000 INFO @ Sat, 11 Dec 2021 11:50:46: 5000000 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 11:50:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.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 11:50:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:50:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:50:57: 3000000 INFO @ Sat, 11 Dec 2021 11:50:58: 6000000 INFO @ Sat, 11 Dec 2021 11:51:00: 1000000 INFO @ Sat, 11 Dec 2021 11:51:09: 4000000 INFO @ Sat, 11 Dec 2021 11:51:10: 7000000 INFO @ Sat, 11 Dec 2021 11:51:11: 2000000 INFO @ Sat, 11 Dec 2021 11:51:21: 5000000 INFO @ Sat, 11 Dec 2021 11:51:22: 3000000 INFO @ Sat, 11 Dec 2021 11:51:23: 8000000 INFO @ Sat, 11 Dec 2021 11:51:33: 4000000 INFO @ Sat, 11 Dec 2021 11:51:35: 9000000 INFO @ Sat, 11 Dec 2021 11:51:35: 6000000 INFO @ Sat, 11 Dec 2021 11:51:43: 5000000 INFO @ Sat, 11 Dec 2021 11:51:47: 10000000 INFO @ Sat, 11 Dec 2021 11:51:48: 7000000 INFO @ Sat, 11 Dec 2021 11:51:53: 6000000 INFO @ Sat, 11 Dec 2021 11:52:01: 11000000 INFO @ Sat, 11 Dec 2021 11:52:01: 8000000 INFO @ Sat, 11 Dec 2021 11:52:04: 7000000 INFO @ Sat, 11 Dec 2021 11:52:14: 12000000 INFO @ Sat, 11 Dec 2021 11:52:14: 9000000 INFO @ Sat, 11 Dec 2021 11:52:15: 8000000 INFO @ Sat, 11 Dec 2021 11:52:24: 9000000 INFO @ Sat, 11 Dec 2021 11:52:25: 13000000 INFO @ Sat, 11 Dec 2021 11:52:25: 10000000 INFO @ Sat, 11 Dec 2021 11:52:34: 10000000 INFO @ Sat, 11 Dec 2021 11:52:36: 14000000 INFO @ Sat, 11 Dec 2021 11:52:36: 11000000 INFO @ Sat, 11 Dec 2021 11:52:44: 11000000 INFO @ Sat, 11 Dec 2021 11:52:47: 15000000 INFO @ Sat, 11 Dec 2021 11:52:48: 12000000 INFO @ Sat, 11 Dec 2021 11:52:48: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:52:48: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:52:48: #1 total tags in treatment: 6604912 INFO @ Sat, 11 Dec 2021 11:52:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:48: #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 11:52:48: #1 tags after filtering in treatment: 5676684 INFO @ Sat, 11 Dec 2021 11:52:48: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 11:52:48: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:49: #2 number of paired peaks: 6289 INFO @ Sat, 11 Dec 2021 11:52:49: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:49: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:49: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:49: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:49: #2 predicted fragment length is 212 bps INFO @ Sat, 11 Dec 2021 11:52:49: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 11 Dec 2021 11:52:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.05_model.r WARNING @ Sat, 11 Dec 2021 11:52:49: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:52:49: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 11 Dec 2021 11:52:49: #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 11:52:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:52:54: 12000000 INFO @ Sat, 11 Dec 2021 11:53:00: 13000000 INFO @ Sat, 11 Dec 2021 11:53:03: 13000000 INFO @ Sat, 11 Dec 2021 11:53:11: 14000000 INFO @ Sat, 11 Dec 2021 11:53:12: 14000000 INFO @ Sat, 11 Dec 2021 11:53:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:22: 15000000 INFO @ Sat, 11 Dec 2021 11:53:23: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:53:23: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:53:23: #1 total tags in treatment: 6604912 INFO @ Sat, 11 Dec 2021 11:53:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:53:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:53:23: #1 tags after filtering in treatment: 5676684 INFO @ Sat, 11 Dec 2021 11:53:23: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 11:53:23: #1 finished! INFO @ Sat, 11 Dec 2021 11:53:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:53:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:53:23: 15000000 INFO @ Sat, 11 Dec 2021 11:53:24: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:53:24: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:53:24: #1 total tags in treatment: 6604912 INFO @ Sat, 11 Dec 2021 11:53:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:53:24: #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 11:53:24: #2 number of paired peaks: 6289 INFO @ Sat, 11 Dec 2021 11:53:24: start model_add_line... INFO @ Sat, 11 Dec 2021 11:53:24: #1 tags after filtering in treatment: 5676684 INFO @ Sat, 11 Dec 2021 11:53:24: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 11:53:24: #1 finished! INFO @ Sat, 11 Dec 2021 11:53:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:53:24: start X-correlation... INFO @ Sat, 11 Dec 2021 11:53:24: end of X-cor INFO @ Sat, 11 Dec 2021 11:53:24: #2 finished! INFO @ Sat, 11 Dec 2021 11:53:24: #2 predicted fragment length is 212 bps INFO @ Sat, 11 Dec 2021 11:53:24: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 11 Dec 2021 11:53:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.20_model.r WARNING @ Sat, 11 Dec 2021 11:53:24: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:53:24: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 11 Dec 2021 11:53:24: #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 11:53:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:53:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:53:25: #2 number of paired peaks: 6289 INFO @ Sat, 11 Dec 2021 11:53:25: start model_add_line... INFO @ Sat, 11 Dec 2021 11:53:25: start X-correlation... INFO @ Sat, 11 Dec 2021 11:53:25: end of X-cor INFO @ Sat, 11 Dec 2021 11:53:25: #2 finished! INFO @ Sat, 11 Dec 2021 11:53:25: #2 predicted fragment length is 212 bps INFO @ Sat, 11 Dec 2021 11:53:25: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 11 Dec 2021 11:53:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.10_model.r WARNING @ Sat, 11 Dec 2021 11:53:25: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:53:25: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 11 Dec 2021 11:53:25: #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 11:53:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:53:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:53:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.05_summits.bed INFO @ Sat, 11 Dec 2021 11:53:26: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (7655 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:53:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.20_summits.bed INFO @ Sat, 11 Dec 2021 11:53:59: Done! BigWig に変換しました。 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3714 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005665/SRX9005665.10_summits.bed INFO @ Sat, 11 Dec 2021 11:54:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5596 records, 4 fields): 10 millis CompletedMACS2peakCalling