Job ID = 12265231 SRX = SRX4029337 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:03 16157449 reads; of these: 16157449 (100.00%) were paired; of these: 10831677 (67.04%) aligned concordantly 0 times 4566555 (28.26%) aligned concordantly exactly 1 time 759217 (4.70%) aligned concordantly >1 times ---- 10831677 pairs aligned concordantly 0 times; of these: 783926 (7.24%) aligned discordantly 1 time ---- 10047751 pairs aligned 0 times concordantly or discordantly; of these: 20095502 mates make up the pairs; of these: 19400173 (96.54%) aligned 0 times 351330 (1.75%) aligned exactly 1 time 343999 (1.71%) aligned >1 times 39.97% overall alignment rate Time searching: 00:12:03 Overall time: 00:12:03 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 8 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] 3630177 / 6073150 = 0.5977 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:31:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.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 @ Sat, 03 Apr 2021 06:31:47: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:31:47: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:31:58: 1000000 INFO @ Sat, 03 Apr 2021 06:32:08: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.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 @ Sat, 03 Apr 2021 06:32:17: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:32:17: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:32:19: 3000000 INFO @ Sat, 03 Apr 2021 06:32:30: 1000000 INFO @ Sat, 03 Apr 2021 06:32:30: 4000000 INFO @ Sat, 03 Apr 2021 06:32:41: 5000000 INFO @ Sat, 03 Apr 2021 06:32:42: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:32:48: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:32:48: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:32:48: #1 total tags in treatment: 2053083 INFO @ Sat, 03 Apr 2021 06:32:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:32:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:32:48: #1 tags after filtering in treatment: 1263313 INFO @ Sat, 03 Apr 2021 06:32:48: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 03 Apr 2021 06:32:48: #1 finished! INFO @ Sat, 03 Apr 2021 06:32:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:32:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.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 @ Sat, 03 Apr 2021 06:32:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:32:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:32:48: #2 number of paired peaks: 3804 INFO @ Sat, 03 Apr 2021 06:32:48: start model_add_line... INFO @ Sat, 03 Apr 2021 06:32:49: start X-correlation... INFO @ Sat, 03 Apr 2021 06:32:49: end of X-cor INFO @ Sat, 03 Apr 2021 06:32:49: #2 finished! INFO @ Sat, 03 Apr 2021 06:32:49: #2 predicted fragment length is 125 bps INFO @ Sat, 03 Apr 2021 06:32:49: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 03 Apr 2021 06:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.05_model.r WARNING @ Sat, 03 Apr 2021 06:32:49: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:32:49: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Sat, 03 Apr 2021 06:32:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:32:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:32:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.05_summits.bed INFO @ Sat, 03 Apr 2021 06:32:54: Done! INFO @ Sat, 03 Apr 2021 06:32:55: 3000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3274 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:33:01: 1000000 INFO @ Sat, 03 Apr 2021 06:33:06: 4000000 INFO @ Sat, 03 Apr 2021 06:33:13: 2000000 INFO @ Sat, 03 Apr 2021 06:33:17: 5000000 INFO @ Sat, 03 Apr 2021 06:33:24: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:33:24: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:33:24: #1 total tags in treatment: 2053083 INFO @ Sat, 03 Apr 2021 06:33:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:33:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:33:24: #1 tags after filtering in treatment: 1263313 INFO @ Sat, 03 Apr 2021 06:33:24: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 03 Apr 2021 06:33:24: #1 finished! INFO @ Sat, 03 Apr 2021 06:33:24: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:33:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:33:24: #2 number of paired peaks: 3804 INFO @ Sat, 03 Apr 2021 06:33:24: start model_add_line... INFO @ Sat, 03 Apr 2021 06:33:24: start X-correlation... INFO @ Sat, 03 Apr 2021 06:33:24: end of X-cor INFO @ Sat, 03 Apr 2021 06:33:24: #2 finished! INFO @ Sat, 03 Apr 2021 06:33:24: #2 predicted fragment length is 125 bps INFO @ Sat, 03 Apr 2021 06:33:24: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 03 Apr 2021 06:33:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.10_model.r WARNING @ Sat, 03 Apr 2021 06:33:24: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:33:24: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Sat, 03 Apr 2021 06:33:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:33:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:33:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:33:25: 3000000 INFO @ Sat, 03 Apr 2021 06:33:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:33:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:33:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:33:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.10_summits.bed INFO @ Sat, 03 Apr 2021 06:33:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1785 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:33:35: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:33:46: 5000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:33:52: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:33:52: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:33:52: #1 total tags in treatment: 2053083 INFO @ Sat, 03 Apr 2021 06:33:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:33:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:33:52: #1 tags after filtering in treatment: 1263313 INFO @ Sat, 03 Apr 2021 06:33:52: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 03 Apr 2021 06:33:52: #1 finished! INFO @ Sat, 03 Apr 2021 06:33:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:33:53: #2 number of paired peaks: 3804 INFO @ Sat, 03 Apr 2021 06:33:53: start model_add_line... INFO @ Sat, 03 Apr 2021 06:33:53: start X-correlation... INFO @ Sat, 03 Apr 2021 06:33:53: end of X-cor INFO @ Sat, 03 Apr 2021 06:33:53: #2 finished! INFO @ Sat, 03 Apr 2021 06:33:53: #2 predicted fragment length is 125 bps INFO @ Sat, 03 Apr 2021 06:33:53: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 03 Apr 2021 06:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.20_model.r WARNING @ Sat, 03 Apr 2021 06:33:53: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:33:53: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Sat, 03 Apr 2021 06:33:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:33:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:33:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:33:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:33:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:33:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:33:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029337/SRX4029337.20_summits.bed INFO @ Sat, 03 Apr 2021 06:33:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (719 records, 4 fields): 3 millis CompletedMACS2peakCalling