Job ID = 14160695 SRX = SRX9567185 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: 01:01:09 29335074 reads; of these: 29335074 (100.00%) were paired; of these: 8318878 (28.36%) aligned concordantly 0 times 18139205 (61.83%) aligned concordantly exactly 1 time 2876991 (9.81%) aligned concordantly >1 times ---- 8318878 pairs aligned concordantly 0 times; of these: 5833137 (70.12%) aligned discordantly 1 time ---- 2485741 pairs aligned 0 times concordantly or discordantly; of these: 4971482 mates make up the pairs; of these: 2270383 (45.67%) aligned 0 times 1330729 (26.77%) aligned exactly 1 time 1370370 (27.56%) aligned >1 times 96.13% overall alignment rate Time searching: 01:01:09 Overall time: 01:01:09 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 44 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] 20452300 / 26821766 = 0.7625 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 05:00:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.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 @ Thu, 09 Dec 2021 05:00:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 05:00:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 05:00:48: 1000000 INFO @ Thu, 09 Dec 2021 05:00:56: 2000000 INFO @ Thu, 09 Dec 2021 05:01:04: 3000000 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 @ Thu, 09 Dec 2021 05:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.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 @ Thu, 09 Dec 2021 05:01:11: #1 read tag files... INFO @ Thu, 09 Dec 2021 05:01:11: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 05:01:11: 4000000 INFO @ Thu, 09 Dec 2021 05:01:20: 1000000 INFO @ Thu, 09 Dec 2021 05:01:20: 5000000 INFO @ Thu, 09 Dec 2021 05:01:29: 2000000 INFO @ Thu, 09 Dec 2021 05:01:29: 6000000 INFO @ Thu, 09 Dec 2021 05:01:38: 3000000 INFO @ Thu, 09 Dec 2021 05:01:38: 7000000 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 @ Thu, 09 Dec 2021 05:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.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 @ Thu, 09 Dec 2021 05:01:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 05:01:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 05:01:47: 4000000 INFO @ Thu, 09 Dec 2021 05:01:48: 8000000 INFO @ Thu, 09 Dec 2021 05:01:50: 1000000 INFO @ Thu, 09 Dec 2021 05:01:57: 5000000 INFO @ Thu, 09 Dec 2021 05:01:57: 9000000 INFO @ Thu, 09 Dec 2021 05:02:00: 2000000 INFO @ Thu, 09 Dec 2021 05:02:06: 10000000 INFO @ Thu, 09 Dec 2021 05:02:06: 6000000 INFO @ Thu, 09 Dec 2021 05:02:09: 3000000 INFO @ Thu, 09 Dec 2021 05:02:15: 11000000 INFO @ Thu, 09 Dec 2021 05:02:16: 7000000 INFO @ Thu, 09 Dec 2021 05:02:18: 4000000 INFO @ Thu, 09 Dec 2021 05:02:24: 12000000 INFO @ Thu, 09 Dec 2021 05:02:25: 8000000 INFO @ Thu, 09 Dec 2021 05:02:28: 5000000 INFO @ Thu, 09 Dec 2021 05:02:33: 13000000 INFO @ Thu, 09 Dec 2021 05:02:35: 9000000 INFO @ Thu, 09 Dec 2021 05:02:37: 6000000 INFO @ Thu, 09 Dec 2021 05:02:42: 14000000 INFO @ Thu, 09 Dec 2021 05:02:44: 10000000 INFO @ Thu, 09 Dec 2021 05:02:46: 7000000 INFO @ Thu, 09 Dec 2021 05:02:52: 15000000 INFO @ Thu, 09 Dec 2021 05:02:53: 11000000 INFO @ Thu, 09 Dec 2021 05:02:56: 8000000 INFO @ Thu, 09 Dec 2021 05:02:56: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 05:02:56: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 05:02:56: #1 total tags in treatment: 5079128 INFO @ Thu, 09 Dec 2021 05:02:56: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 05:02:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 05:02:56: #1 tags after filtering in treatment: 4561796 INFO @ Thu, 09 Dec 2021 05:02:56: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 05:02:56: #1 finished! INFO @ Thu, 09 Dec 2021 05:02:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 05:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 05:02:56: #2 number of paired peaks: 682 WARNING @ Thu, 09 Dec 2021 05:02:56: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Thu, 09 Dec 2021 05:02:56: start model_add_line... INFO @ Thu, 09 Dec 2021 05:02:56: start X-correlation... INFO @ Thu, 09 Dec 2021 05:02:56: end of X-cor INFO @ Thu, 09 Dec 2021 05:02:56: #2 finished! INFO @ Thu, 09 Dec 2021 05:02:56: #2 predicted fragment length is 228 bps INFO @ Thu, 09 Dec 2021 05:02:56: #2 alternative fragment length(s) may be 228 bps INFO @ Thu, 09 Dec 2021 05:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.05_model.r WARNING @ Thu, 09 Dec 2021 05:02:56: #2 Since the d (228) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 05:02:56: #2 You may need to consider one of the other alternative d(s): 228 WARNING @ Thu, 09 Dec 2021 05:02:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 05:02:56: #3 Call peaks... INFO @ Thu, 09 Dec 2021 05:02:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 05:03:02: 12000000 INFO @ Thu, 09 Dec 2021 05:03:05: 9000000 INFO @ Thu, 09 Dec 2021 05:03:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 05:03:11: 13000000 INFO @ Thu, 09 Dec 2021 05:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.05_peaks.xls INFO @ Thu, 09 Dec 2021 05:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 05:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.05_summits.bed INFO @ Thu, 09 Dec 2021 05:03:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (604 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 05:03:14: 10000000 INFO @ Thu, 09 Dec 2021 05:03:21: 14000000 INFO @ Thu, 09 Dec 2021 05:03:23: 11000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 05:03:30: 15000000 INFO @ Thu, 09 Dec 2021 05:03:32: 12000000 INFO @ Thu, 09 Dec 2021 05:03:34: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 05:03:34: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 05:03:34: #1 total tags in treatment: 5079128 INFO @ Thu, 09 Dec 2021 05:03:34: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 05:03:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 05:03:34: #1 tags after filtering in treatment: 4561796 INFO @ Thu, 09 Dec 2021 05:03:34: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 05:03:34: #1 finished! INFO @ Thu, 09 Dec 2021 05:03:34: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 05:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 05:03:35: #2 number of paired peaks: 682 WARNING @ Thu, 09 Dec 2021 05:03:35: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Thu, 09 Dec 2021 05:03:35: start model_add_line... INFO @ Thu, 09 Dec 2021 05:03:35: start X-correlation... INFO @ Thu, 09 Dec 2021 05:03:35: end of X-cor INFO @ Thu, 09 Dec 2021 05:03:35: #2 finished! INFO @ Thu, 09 Dec 2021 05:03:35: #2 predicted fragment length is 228 bps INFO @ Thu, 09 Dec 2021 05:03:35: #2 alternative fragment length(s) may be 228 bps INFO @ Thu, 09 Dec 2021 05:03:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.10_model.r WARNING @ Thu, 09 Dec 2021 05:03:35: #2 Since the d (228) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 05:03:35: #2 You may need to consider one of the other alternative d(s): 228 WARNING @ Thu, 09 Dec 2021 05:03:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 05:03:35: #3 Call peaks... INFO @ Thu, 09 Dec 2021 05:03:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 05:03:41: 13000000 INFO @ Thu, 09 Dec 2021 05:03:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 05:03:49: 14000000 INFO @ Thu, 09 Dec 2021 05:03:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.10_peaks.xls INFO @ Thu, 09 Dec 2021 05:03:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 05:03:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.10_summits.bed INFO @ Thu, 09 Dec 2021 05:03:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (403 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 05:03:58: 15000000 INFO @ Thu, 09 Dec 2021 05:04:02: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 05:04:02: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 05:04:02: #1 total tags in treatment: 5079128 INFO @ Thu, 09 Dec 2021 05:04:02: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 05:04:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 05:04:02: #1 tags after filtering in treatment: 4561796 INFO @ Thu, 09 Dec 2021 05:04:02: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 05:04:02: #1 finished! INFO @ Thu, 09 Dec 2021 05:04:02: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 05:04:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 05:04:02: #2 number of paired peaks: 682 WARNING @ Thu, 09 Dec 2021 05:04:02: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Thu, 09 Dec 2021 05:04:02: start model_add_line... INFO @ Thu, 09 Dec 2021 05:04:02: start X-correlation... INFO @ Thu, 09 Dec 2021 05:04:02: end of X-cor INFO @ Thu, 09 Dec 2021 05:04:02: #2 finished! INFO @ Thu, 09 Dec 2021 05:04:02: #2 predicted fragment length is 228 bps INFO @ Thu, 09 Dec 2021 05:04:02: #2 alternative fragment length(s) may be 228 bps INFO @ Thu, 09 Dec 2021 05:04:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.20_model.r WARNING @ Thu, 09 Dec 2021 05:04:02: #2 Since the d (228) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 05:04:02: #2 You may need to consider one of the other alternative d(s): 228 WARNING @ Thu, 09 Dec 2021 05:04:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 05:04:02: #3 Call peaks... INFO @ Thu, 09 Dec 2021 05:04:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 05:04:13: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 05:04:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.20_peaks.xls INFO @ Thu, 09 Dec 2021 05:04:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 05:04:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567185/SRX9567185.20_summits.bed INFO @ Thu, 09 Dec 2021 05:04:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (292 records, 4 fields): 2 millis CompletedMACS2peakCalling