Job ID = 12265636 SRX = SRX7246266 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: 00:56:15 32073993 reads; of these: 32073993 (100.00%) were paired; of these: 18461326 (57.56%) aligned concordantly 0 times 12338518 (38.47%) aligned concordantly exactly 1 time 1274149 (3.97%) aligned concordantly >1 times ---- 18461326 pairs aligned concordantly 0 times; of these: 4855555 (26.30%) aligned discordantly 1 time ---- 13605771 pairs aligned 0 times concordantly or discordantly; of these: 27211542 mates make up the pairs; of these: 25572491 (93.98%) aligned 0 times 842471 (3.10%) aligned exactly 1 time 796580 (2.93%) aligned >1 times 60.14% overall alignment rate Time searching: 00:56:16 Overall time: 00:56:16 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 28 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] 14836732 / 18324547 = 0.8097 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 09:04:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.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 09:04:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:04:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:04:57: 1000000 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 09:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.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 09:05:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:05:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:05:12: 2000000 INFO @ Sat, 03 Apr 2021 09:05:28: 1000000 INFO @ Sat, 03 Apr 2021 09:05:29: 3000000 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 09:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.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 09:05:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:05:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:05:44: 2000000 INFO @ Sat, 03 Apr 2021 09:05:45: 4000000 INFO @ Sat, 03 Apr 2021 09:05:57: 1000000 INFO @ Sat, 03 Apr 2021 09:06:00: 3000000 INFO @ Sat, 03 Apr 2021 09:06:01: 5000000 INFO @ Sat, 03 Apr 2021 09:06:13: 2000000 INFO @ Sat, 03 Apr 2021 09:06:16: 4000000 INFO @ Sat, 03 Apr 2021 09:06:17: 6000000 INFO @ Sat, 03 Apr 2021 09:06:28: 3000000 INFO @ Sat, 03 Apr 2021 09:06:31: 5000000 INFO @ Sat, 03 Apr 2021 09:06:32: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:06:43: 4000000 INFO @ Sat, 03 Apr 2021 09:06:47: 6000000 INFO @ Sat, 03 Apr 2021 09:06:48: 8000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:06:59: 5000000 INFO @ Sat, 03 Apr 2021 09:07:01: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 09:07:01: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 09:07:01: #1 total tags in treatment: 2383497 INFO @ Sat, 03 Apr 2021 09:07:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:07:01: #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 09:07:01: #1 tags after filtering in treatment: 1635240 INFO @ Sat, 03 Apr 2021 09:07:01: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 03 Apr 2021 09:07:01: #1 finished! INFO @ Sat, 03 Apr 2021 09:07:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:07:01: #2 number of paired peaks: 2333 INFO @ Sat, 03 Apr 2021 09:07:01: start model_add_line... INFO @ Sat, 03 Apr 2021 09:07:01: start X-correlation... INFO @ Sat, 03 Apr 2021 09:07:01: end of X-cor INFO @ Sat, 03 Apr 2021 09:07:01: #2 finished! INFO @ Sat, 03 Apr 2021 09:07:01: #2 predicted fragment length is 216 bps INFO @ Sat, 03 Apr 2021 09:07:01: #2 alternative fragment length(s) may be 216 bps INFO @ Sat, 03 Apr 2021 09:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.05_model.r WARNING @ Sat, 03 Apr 2021 09:07:01: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:07:01: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Sat, 03 Apr 2021 09:07:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:07:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:07:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:07:02: 7000000 INFO @ Sat, 03 Apr 2021 09:07:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:07:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:07:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:07:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.05_summits.bed INFO @ Sat, 03 Apr 2021 09:07:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2478 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:07:14: 6000000 INFO @ Sat, 03 Apr 2021 09:07:18: 8000000 INFO @ Sat, 03 Apr 2021 09:07:28: 7000000 INFO @ Sat, 03 Apr 2021 09:07:30: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 09:07:30: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 09:07:30: #1 total tags in treatment: 2383497 INFO @ Sat, 03 Apr 2021 09:07:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:07:30: #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 09:07:30: #1 tags after filtering in treatment: 1635240 INFO @ Sat, 03 Apr 2021 09:07:30: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 03 Apr 2021 09:07:30: #1 finished! INFO @ Sat, 03 Apr 2021 09:07:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:07:30: #2 number of paired peaks: 2333 INFO @ Sat, 03 Apr 2021 09:07:30: start model_add_line... INFO @ Sat, 03 Apr 2021 09:07:30: start X-correlation... INFO @ Sat, 03 Apr 2021 09:07:30: end of X-cor INFO @ Sat, 03 Apr 2021 09:07:30: #2 finished! INFO @ Sat, 03 Apr 2021 09:07:30: #2 predicted fragment length is 216 bps INFO @ Sat, 03 Apr 2021 09:07:30: #2 alternative fragment length(s) may be 216 bps INFO @ Sat, 03 Apr 2021 09:07:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.10_model.r WARNING @ Sat, 03 Apr 2021 09:07:30: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:07:30: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Sat, 03 Apr 2021 09:07:30: #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 09:07:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:07:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:07:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:07:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:07:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:07:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.10_summits.bed INFO @ Sat, 03 Apr 2021 09:07:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1503 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:07:41: 8000000 INFO @ Sat, 03 Apr 2021 09:07:52: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 09:07:52: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 09:07:52: #1 total tags in treatment: 2383497 INFO @ Sat, 03 Apr 2021 09:07:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:07:52: #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 09:07:52: #1 tags after filtering in treatment: 1635240 INFO @ Sat, 03 Apr 2021 09:07:52: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 03 Apr 2021 09:07:52: #1 finished! INFO @ Sat, 03 Apr 2021 09:07:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:07:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:07:52: #2 number of paired peaks: 2333 INFO @ Sat, 03 Apr 2021 09:07:52: start model_add_line... INFO @ Sat, 03 Apr 2021 09:07:52: start X-correlation... INFO @ Sat, 03 Apr 2021 09:07:52: end of X-cor INFO @ Sat, 03 Apr 2021 09:07:52: #2 finished! INFO @ Sat, 03 Apr 2021 09:07:52: #2 predicted fragment length is 216 bps INFO @ Sat, 03 Apr 2021 09:07:52: #2 alternative fragment length(s) may be 216 bps INFO @ Sat, 03 Apr 2021 09:07:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.20_model.r WARNING @ Sat, 03 Apr 2021 09:07:52: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:07:52: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Sat, 03 Apr 2021 09:07:52: #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 09:07:52: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:07:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:07:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:07:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:07:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:07:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246266/SRX7246266.20_summits.bed INFO @ Sat, 03 Apr 2021 09:07:59: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (770 records, 4 fields): 4 millis CompletedMACS2peakCalling