Job ID = 14159339 SRX = SRX10641190 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: 00:27:11 25750545 reads; of these: 25750545 (100.00%) were paired; of these: 17341034 (67.34%) aligned concordantly 0 times 7436950 (28.88%) aligned concordantly exactly 1 time 972561 (3.78%) aligned concordantly >1 times ---- 17341034 pairs aligned concordantly 0 times; of these: 2941028 (16.96%) aligned discordantly 1 time ---- 14400006 pairs aligned 0 times concordantly or discordantly; of these: 28800012 mates make up the pairs; of these: 27429203 (95.24%) aligned 0 times 753136 (2.62%) aligned exactly 1 time 617673 (2.14%) aligned >1 times 46.74% overall alignment rate Time searching: 00:27:11 Overall time: 00:27:11 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 20 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] 1611024 / 11313747 = 0.1424 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 @ Wed, 08 Dec 2021 21:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.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 @ Wed, 08 Dec 2021 21:44:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:44:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:44:10: 1000000 INFO @ Wed, 08 Dec 2021 21:44:17: 2000000 INFO @ Wed, 08 Dec 2021 21:44:25: 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 @ Wed, 08 Dec 2021 21:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.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 @ Wed, 08 Dec 2021 21:44:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:44:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:44:32: 4000000 INFO @ Wed, 08 Dec 2021 21:44:41: 5000000 INFO @ Wed, 08 Dec 2021 21:44:42: 1000000 INFO @ Wed, 08 Dec 2021 21:44:49: 6000000 INFO @ Wed, 08 Dec 2021 21:44:52: 2000000 INFO @ Wed, 08 Dec 2021 21:44:58: 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 @ Wed, 08 Dec 2021 21:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.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 @ Wed, 08 Dec 2021 21:45:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:45:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:45:02: 3000000 INFO @ Wed, 08 Dec 2021 21:45:07: 8000000 INFO @ Wed, 08 Dec 2021 21:45:11: 1000000 INFO @ Wed, 08 Dec 2021 21:45:12: 4000000 INFO @ Wed, 08 Dec 2021 21:45:16: 9000000 INFO @ Wed, 08 Dec 2021 21:45:21: 5000000 INFO @ Wed, 08 Dec 2021 21:45:21: 2000000 INFO @ Wed, 08 Dec 2021 21:45:25: 10000000 INFO @ Wed, 08 Dec 2021 21:45:30: 6000000 INFO @ Wed, 08 Dec 2021 21:45:31: 3000000 INFO @ Wed, 08 Dec 2021 21:45:34: 11000000 INFO @ Wed, 08 Dec 2021 21:45:39: 7000000 INFO @ Wed, 08 Dec 2021 21:45:41: 4000000 INFO @ Wed, 08 Dec 2021 21:45:43: 12000000 INFO @ Wed, 08 Dec 2021 21:45:48: 8000000 INFO @ Wed, 08 Dec 2021 21:45:50: 5000000 INFO @ Wed, 08 Dec 2021 21:45:52: 13000000 INFO @ Wed, 08 Dec 2021 21:45:57: 9000000 INFO @ Wed, 08 Dec 2021 21:46:00: 6000000 INFO @ Wed, 08 Dec 2021 21:46:01: 14000000 INFO @ Wed, 08 Dec 2021 21:46:06: 10000000 INFO @ Wed, 08 Dec 2021 21:46:10: 7000000 INFO @ Wed, 08 Dec 2021 21:46:10: 15000000 INFO @ Wed, 08 Dec 2021 21:46:15: 11000000 INFO @ Wed, 08 Dec 2021 21:46:19: 8000000 INFO @ Wed, 08 Dec 2021 21:46:19: 16000000 INFO @ Wed, 08 Dec 2021 21:46:24: 12000000 INFO @ Wed, 08 Dec 2021 21:46:29: 17000000 INFO @ Wed, 08 Dec 2021 21:46:29: 9000000 INFO @ Wed, 08 Dec 2021 21:46:33: 13000000 INFO @ Wed, 08 Dec 2021 21:46:38: 18000000 INFO @ Wed, 08 Dec 2021 21:46:38: 10000000 INFO @ Wed, 08 Dec 2021 21:46:42: 14000000 INFO @ Wed, 08 Dec 2021 21:46:47: 19000000 INFO @ Wed, 08 Dec 2021 21:46:48: 11000000 INFO @ Wed, 08 Dec 2021 21:46:52: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:46:56: 20000000 INFO @ Wed, 08 Dec 2021 21:46:58: 12000000 INFO @ Wed, 08 Dec 2021 21:47:01: 16000000 INFO @ Wed, 08 Dec 2021 21:47:04: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 21:47:04: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 21:47:04: #1 total tags in treatment: 7132730 INFO @ Wed, 08 Dec 2021 21:47:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:47:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:47:04: #1 tags after filtering in treatment: 6546065 INFO @ Wed, 08 Dec 2021 21:47:04: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:47:04: #1 finished! INFO @ Wed, 08 Dec 2021 21:47:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:47:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:47:04: #2 number of paired peaks: 1703 INFO @ Wed, 08 Dec 2021 21:47:04: start model_add_line... INFO @ Wed, 08 Dec 2021 21:47:05: start X-correlation... INFO @ Wed, 08 Dec 2021 21:47:05: end of X-cor INFO @ Wed, 08 Dec 2021 21:47:05: #2 finished! INFO @ Wed, 08 Dec 2021 21:47:05: #2 predicted fragment length is 247 bps INFO @ Wed, 08 Dec 2021 21:47:05: #2 alternative fragment length(s) may be 4,247 bps INFO @ Wed, 08 Dec 2021 21:47:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.05_model.r WARNING @ Wed, 08 Dec 2021 21:47:05: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:47:05: #2 You may need to consider one of the other alternative d(s): 4,247 WARNING @ Wed, 08 Dec 2021 21:47:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:47:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:47:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:47:07: 13000000 INFO @ Wed, 08 Dec 2021 21:47:10: 17000000 INFO @ Wed, 08 Dec 2021 21:47:17: 14000000 INFO @ Wed, 08 Dec 2021 21:47:19: 18000000 INFO @ Wed, 08 Dec 2021 21:47:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:47:27: 15000000 INFO @ Wed, 08 Dec 2021 21:47:28: 19000000 INFO @ Wed, 08 Dec 2021 21:47:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:47:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:47:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.05_summits.bed INFO @ Wed, 08 Dec 2021 21:47:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2512 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:47:36: 16000000 INFO @ Wed, 08 Dec 2021 21:47:37: 20000000 INFO @ Wed, 08 Dec 2021 21:47:44: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 21:47:44: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 21:47:44: #1 total tags in treatment: 7132730 INFO @ Wed, 08 Dec 2021 21:47:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:47:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:47:44: #1 tags after filtering in treatment: 6546065 INFO @ Wed, 08 Dec 2021 21:47:44: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:47:44: #1 finished! INFO @ Wed, 08 Dec 2021 21:47:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:47:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:47:45: #2 number of paired peaks: 1703 INFO @ Wed, 08 Dec 2021 21:47:45: start model_add_line... INFO @ Wed, 08 Dec 2021 21:47:45: start X-correlation... INFO @ Wed, 08 Dec 2021 21:47:45: end of X-cor INFO @ Wed, 08 Dec 2021 21:47:45: #2 finished! INFO @ Wed, 08 Dec 2021 21:47:45: #2 predicted fragment length is 247 bps INFO @ Wed, 08 Dec 2021 21:47:45: #2 alternative fragment length(s) may be 4,247 bps INFO @ Wed, 08 Dec 2021 21:47:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.10_model.r WARNING @ Wed, 08 Dec 2021 21:47:45: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:47:45: #2 You may need to consider one of the other alternative d(s): 4,247 WARNING @ Wed, 08 Dec 2021 21:47:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:47:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:47:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:47:46: 17000000 INFO @ Wed, 08 Dec 2021 21:47:55: 18000000 INFO @ Wed, 08 Dec 2021 21:48:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:48:04: 19000000 INFO @ Wed, 08 Dec 2021 21:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.10_summits.bed INFO @ Wed, 08 Dec 2021 21:48:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1138 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:48:13: 20000000 INFO @ Wed, 08 Dec 2021 21:48:20: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 21:48:20: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 21:48:20: #1 total tags in treatment: 7132730 INFO @ Wed, 08 Dec 2021 21:48:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:48:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:48:20: #1 tags after filtering in treatment: 6546065 INFO @ Wed, 08 Dec 2021 21:48:20: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:48:20: #1 finished! INFO @ Wed, 08 Dec 2021 21:48:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:48:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:48:21: #2 number of paired peaks: 1703 INFO @ Wed, 08 Dec 2021 21:48:21: start model_add_line... INFO @ Wed, 08 Dec 2021 21:48:21: start X-correlation... INFO @ Wed, 08 Dec 2021 21:48:21: end of X-cor INFO @ Wed, 08 Dec 2021 21:48:21: #2 finished! INFO @ Wed, 08 Dec 2021 21:48:21: #2 predicted fragment length is 247 bps INFO @ Wed, 08 Dec 2021 21:48:21: #2 alternative fragment length(s) may be 4,247 bps INFO @ Wed, 08 Dec 2021 21:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.20_model.r WARNING @ Wed, 08 Dec 2021 21:48:21: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:48:21: #2 You may need to consider one of the other alternative d(s): 4,247 WARNING @ Wed, 08 Dec 2021 21:48:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:48:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:48:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:48:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:48:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:48:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641190/SRX10641190.20_summits.bed INFO @ Wed, 08 Dec 2021 21:48:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (485 records, 4 fields): 2 millis CompletedMACS2peakCalling