Job ID = 14171318 SRX = SRX9005670 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1201753 READS because READLEN < 1 Read 9542968 spots for SRR12515071/SRR12515071.sra Written 9542968 spots for SRR12515071/SRR12515071.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171866 ("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] 1 unmatched pairs [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] 2 unmatched pairs [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] 8 unmatched pairs [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] 10 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] 3 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1261564 / 7158984 = 0.1762 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 11:43:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.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 11:43:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:43:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:43:45: 1000000 INFO @ Sat, 11 Dec 2021 11:43:51: 2000000 INFO @ Sat, 11 Dec 2021 11:43:57: 3000000 INFO @ Sat, 11 Dec 2021 11:44:03: 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 11:44:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.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 11:44:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:44:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:44:09: 5000000 INFO @ Sat, 11 Dec 2021 11:44:15: 1000000 INFO @ Sat, 11 Dec 2021 11:44:16: 6000000 INFO @ Sat, 11 Dec 2021 11:44:21: 2000000 INFO @ Sat, 11 Dec 2021 11:44:22: 7000000 INFO @ Sat, 11 Dec 2021 11:44:27: 3000000 INFO @ Sat, 11 Dec 2021 11:44:28: 8000000 INFO @ Sat, 11 Dec 2021 11:44:33: 4000000 INFO @ Sat, 11 Dec 2021 11:44:34: 9000000 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 11:44:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.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 11:44:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:44:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:44:39: 5000000 INFO @ Sat, 11 Dec 2021 11:44:40: 10000000 INFO @ Sat, 11 Dec 2021 11:44:45: 1000000 INFO @ Sat, 11 Dec 2021 11:44:45: 6000000 INFO @ Sat, 11 Dec 2021 11:44:46: 11000000 INFO @ Sat, 11 Dec 2021 11:44:51: 7000000 INFO @ Sat, 11 Dec 2021 11:44:51: 2000000 INFO @ Sat, 11 Dec 2021 11:44:53: 12000000 INFO @ Sat, 11 Dec 2021 11:44:57: 8000000 INFO @ Sat, 11 Dec 2021 11:44:57: 3000000 INFO @ Sat, 11 Dec 2021 11:44:59: 13000000 INFO @ Sat, 11 Dec 2021 11:45:00: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 11:45:00: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 11:45:00: #1 total tags in treatment: 5784325 INFO @ Sat, 11 Dec 2021 11:45:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:45:00: #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 11:45:00: #1 tags after filtering in treatment: 4752376 INFO @ Sat, 11 Dec 2021 11:45:00: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 11:45:00: #1 finished! INFO @ Sat, 11 Dec 2021 11:45:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:45:01: #2 number of paired peaks: 7487 INFO @ Sat, 11 Dec 2021 11:45:01: start model_add_line... INFO @ Sat, 11 Dec 2021 11:45:01: start X-correlation... INFO @ Sat, 11 Dec 2021 11:45:01: end of X-cor INFO @ Sat, 11 Dec 2021 11:45:01: #2 finished! INFO @ Sat, 11 Dec 2021 11:45:01: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 11:45:01: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 11:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.05_model.r WARNING @ Sat, 11 Dec 2021 11:45:01: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:45:01: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Sat, 11 Dec 2021 11:45:01: #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 11:45:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:45:03: 9000000 INFO @ Sat, 11 Dec 2021 11:45:03: 4000000 INFO @ Sat, 11 Dec 2021 11:45:09: 10000000 INFO @ Sat, 11 Dec 2021 11:45:09: 5000000 INFO @ Sat, 11 Dec 2021 11:45:15: 6000000 INFO @ Sat, 11 Dec 2021 11:45:16: 11000000 INFO @ Sat, 11 Dec 2021 11:45:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:45:21: 7000000 INFO @ Sat, 11 Dec 2021 11:45:22: 12000000 INFO @ Sat, 11 Dec 2021 11:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.05_summits.bed INFO @ Sat, 11 Dec 2021 11:45:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7672 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:45:27: 8000000 INFO @ Sat, 11 Dec 2021 11:45:27: 13000000 INFO @ Sat, 11 Dec 2021 11:45:29: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 11:45:29: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 11:45:29: #1 total tags in treatment: 5784325 INFO @ Sat, 11 Dec 2021 11:45:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:45:29: #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 11:45:29: #1 tags after filtering in treatment: 4752376 INFO @ Sat, 11 Dec 2021 11:45:29: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 11:45:29: #1 finished! INFO @ Sat, 11 Dec 2021 11:45:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:45:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:45:29: #2 number of paired peaks: 7487 INFO @ Sat, 11 Dec 2021 11:45:29: start model_add_line... INFO @ Sat, 11 Dec 2021 11:45:29: start X-correlation... INFO @ Sat, 11 Dec 2021 11:45:29: end of X-cor INFO @ Sat, 11 Dec 2021 11:45:29: #2 finished! INFO @ Sat, 11 Dec 2021 11:45:29: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 11:45:29: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 11:45:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.10_model.r WARNING @ Sat, 11 Dec 2021 11:45:29: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:45:29: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Sat, 11 Dec 2021 11:45:29: #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 11:45:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:45:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:45:33: 9000000 INFO @ Sat, 11 Dec 2021 11:45:39: 10000000 INFO @ Sat, 11 Dec 2021 11:45:43: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:45:45: 11000000 INFO @ Sat, 11 Dec 2021 11:45:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:45:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:45:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.10_summits.bed INFO @ Sat, 11 Dec 2021 11:45:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6114 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:45:50: 12000000 INFO @ Sat, 11 Dec 2021 11:45:56: 13000000 INFO @ Sat, 11 Dec 2021 11:45:57: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 11:45:57: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 11:45:57: #1 total tags in treatment: 5784325 INFO @ Sat, 11 Dec 2021 11:45:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:45:57: #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 11:45:57: #1 tags after filtering in treatment: 4752376 INFO @ Sat, 11 Dec 2021 11:45:57: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 11:45:57: #1 finished! INFO @ Sat, 11 Dec 2021 11:45:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:45:58: #2 number of paired peaks: 7487 INFO @ Sat, 11 Dec 2021 11:45:58: start model_add_line... INFO @ Sat, 11 Dec 2021 11:45:58: start X-correlation... INFO @ Sat, 11 Dec 2021 11:45:58: end of X-cor INFO @ Sat, 11 Dec 2021 11:45:58: #2 finished! INFO @ Sat, 11 Dec 2021 11:45:58: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 11:45:58: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 11:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.20_model.r WARNING @ Sat, 11 Dec 2021 11:45:58: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:45:58: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Sat, 11 Dec 2021 11:45:58: #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 11:45:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:45:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:46:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:46:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:46:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:46:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005670/SRX9005670.20_summits.bed INFO @ Sat, 11 Dec 2021 11:46:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4394 records, 4 fields): 6 millis CompletedMACS2peakCalling