Job ID = 16432581 SRX = SRX9091662 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 86 READS because READLEN < 1 Read 55820009 spots for SRR12608197/SRR12608197.sra Written 55820009 spots for SRR12608197/SRR12608197.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436156 ("srTce11") 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 -1 than in file specified with -2 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: 7 sequences. [bam_sort_core] merging from 48 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 51343313 / 53867634 = 0.9531 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:19:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 02 Aug 2022 11:19:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:19:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:19:24: 1000000 INFO @ Tue, 02 Aug 2022 11:19:33: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:19:42: 3000000 INFO @ Tue, 02 Aug 2022 11:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 02 Aug 2022 11:19:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:19:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:19:51: 4000000 INFO @ Tue, 02 Aug 2022 11:19:52: 1000000 INFO @ Tue, 02 Aug 2022 11:20:00: 5000000 INFO @ Tue, 02 Aug 2022 11:20:01: 2000000 INFO @ Tue, 02 Aug 2022 11:20:06: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:20:06: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:20:06: #1 total tags in treatment: 2528252 INFO @ Tue, 02 Aug 2022 11:20:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:20:06: #1 tags after filtering in treatment: 2111644 INFO @ Tue, 02 Aug 2022 11:20:06: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 11:20:06: #1 finished! INFO @ Tue, 02 Aug 2022 11:20:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:20:07: #2 number of paired peaks: 1338 INFO @ Tue, 02 Aug 2022 11:20:07: start model_add_line... INFO @ Tue, 02 Aug 2022 11:20:07: start X-correlation... INFO @ Tue, 02 Aug 2022 11:20:07: end of X-cor INFO @ Tue, 02 Aug 2022 11:20:07: #2 finished! INFO @ Tue, 02 Aug 2022 11:20:07: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 11:20:07: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 11:20:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.05_model.r WARNING @ Tue, 02 Aug 2022 11:20:07: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:20:07: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 11:20:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:20:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:20:07: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Tue, 02 Aug 2022 11:20:11: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:20:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 02 Aug 2022 11:20:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:20:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:20:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:20:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:20:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.05_summits.bed INFO @ Tue, 02 Aug 2022 11:20:16: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (846 records, 4 fields): 111 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:20:20: 4000000 INFO @ Tue, 02 Aug 2022 11:20:22: 1000000 INFO @ Tue, 02 Aug 2022 11:20:29: 5000000 INFO @ Tue, 02 Aug 2022 11:20:32: 2000000 INFO @ Tue, 02 Aug 2022 11:20:36: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:20:36: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:20:36: #1 total tags in treatment: 2528252 INFO @ Tue, 02 Aug 2022 11:20:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:20:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:20:36: #1 tags after filtering in treatment: 2111644 INFO @ Tue, 02 Aug 2022 11:20:36: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 11:20:36: #1 finished! INFO @ Tue, 02 Aug 2022 11:20:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:20:36: #2 number of paired peaks: 1338 INFO @ Tue, 02 Aug 2022 11:20:36: start model_add_line... INFO @ Tue, 02 Aug 2022 11:20:36: start X-correlation... INFO @ Tue, 02 Aug 2022 11:20:36: end of X-cor INFO @ Tue, 02 Aug 2022 11:20:36: #2 finished! INFO @ Tue, 02 Aug 2022 11:20:36: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 11:20:36: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 11:20:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.10_model.r WARNING @ Tue, 02 Aug 2022 11:20:36: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:20:36: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 11:20:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:20:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:20:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:20:41: 3000000 INFO @ Tue, 02 Aug 2022 11:20:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.10_summits.bed INFO @ Tue, 02 Aug 2022 11:20:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (528 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:20:50: 4000000 INFO @ Tue, 02 Aug 2022 11:20:57: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:21:03: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:21:03: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:21:03: #1 total tags in treatment: 2528252 INFO @ Tue, 02 Aug 2022 11:21:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:21:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:21:03: #1 tags after filtering in treatment: 2111644 INFO @ Tue, 02 Aug 2022 11:21:03: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 11:21:03: #1 finished! INFO @ Tue, 02 Aug 2022 11:21:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:21:04: #2 number of paired peaks: 1338 INFO @ Tue, 02 Aug 2022 11:21:04: start model_add_line... INFO @ Tue, 02 Aug 2022 11:21:04: start X-correlation... INFO @ Tue, 02 Aug 2022 11:21:04: end of X-cor INFO @ Tue, 02 Aug 2022 11:21:04: #2 finished! INFO @ Tue, 02 Aug 2022 11:21:04: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 11:21:04: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 11:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.20_model.r WARNING @ Tue, 02 Aug 2022 11:21:04: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:21:04: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 11:21:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:21:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:21:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9091662/SRX9091662.20_summits.bed INFO @ Tue, 02 Aug 2022 11:21:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (307 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。