Job ID = 14159004 SRX = SRX10641180 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: 00:21:51 18376068 reads; of these: 18376068 (100.00%) were paired; of these: 11311919 (61.56%) aligned concordantly 0 times 6301980 (34.29%) aligned concordantly exactly 1 time 762169 (4.15%) aligned concordantly >1 times ---- 11311919 pairs aligned concordantly 0 times; of these: 2945097 (26.04%) aligned discordantly 1 time ---- 8366822 pairs aligned 0 times concordantly or discordantly; of these: 16733644 mates make up the pairs; of these: 15534249 (92.83%) aligned 0 times 645036 (3.85%) aligned exactly 1 time 554359 (3.31%) aligned >1 times 57.73% overall alignment rate Time searching: 00:21:51 Overall time: 00:21:51 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 16 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] 1193478 / 9987330 = 0.1195 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 19:07:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.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 19:07:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:07:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:07:38: 1000000 INFO @ Wed, 08 Dec 2021 19:07:45: 2000000 INFO @ Wed, 08 Dec 2021 19:07:52: 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 19:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.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 19:07:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:07:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:08:00: 4000000 INFO @ Wed, 08 Dec 2021 19:08:09: 5000000 INFO @ Wed, 08 Dec 2021 19:08:10: 1000000 INFO @ Wed, 08 Dec 2021 19:08:18: 6000000 INFO @ Wed, 08 Dec 2021 19:08:21: 2000000 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 19:08:28: 7000000 INFO @ Wed, 08 Dec 2021 19:08:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.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 19:08:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:08:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:08:31: 3000000 INFO @ Wed, 08 Dec 2021 19:08:37: 8000000 INFO @ Wed, 08 Dec 2021 19:08:39: 1000000 INFO @ Wed, 08 Dec 2021 19:08:42: 4000000 INFO @ Wed, 08 Dec 2021 19:08:47: 9000000 INFO @ Wed, 08 Dec 2021 19:08:48: 2000000 INFO @ Wed, 08 Dec 2021 19:08:54: 5000000 INFO @ Wed, 08 Dec 2021 19:08:57: 10000000 INFO @ Wed, 08 Dec 2021 19:08:58: 3000000 INFO @ Wed, 08 Dec 2021 19:09:04: 6000000 INFO @ Wed, 08 Dec 2021 19:09:07: 11000000 INFO @ Wed, 08 Dec 2021 19:09:08: 4000000 INFO @ Wed, 08 Dec 2021 19:09:15: 7000000 INFO @ Wed, 08 Dec 2021 19:09:16: 12000000 INFO @ Wed, 08 Dec 2021 19:09:18: 5000000 INFO @ Wed, 08 Dec 2021 19:09:26: 13000000 INFO @ Wed, 08 Dec 2021 19:09:27: 8000000 INFO @ Wed, 08 Dec 2021 19:09:28: 6000000 INFO @ Wed, 08 Dec 2021 19:09:36: 14000000 INFO @ Wed, 08 Dec 2021 19:09:38: 7000000 INFO @ Wed, 08 Dec 2021 19:09:38: 9000000 INFO @ Wed, 08 Dec 2021 19:09:46: 15000000 INFO @ Wed, 08 Dec 2021 19:09:48: 8000000 INFO @ Wed, 08 Dec 2021 19:09:49: 10000000 INFO @ Wed, 08 Dec 2021 19:09:56: 16000000 INFO @ Wed, 08 Dec 2021 19:09:57: 9000000 INFO @ Wed, 08 Dec 2021 19:10:00: 11000000 INFO @ Wed, 08 Dec 2021 19:10:06: 17000000 INFO @ Wed, 08 Dec 2021 19:10:07: 10000000 INFO @ Wed, 08 Dec 2021 19:10:12: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:10:16: 18000000 INFO @ Wed, 08 Dec 2021 19:10:17: 11000000 INFO @ Wed, 08 Dec 2021 19:10:23: 13000000 INFO @ Wed, 08 Dec 2021 19:10:24: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:10:24: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:10:24: #1 total tags in treatment: 6137879 INFO @ Wed, 08 Dec 2021 19:10:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:10:24: #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 19:10:24: #1 tags after filtering in treatment: 5714816 INFO @ Wed, 08 Dec 2021 19:10:24: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:10:24: #1 finished! INFO @ Wed, 08 Dec 2021 19:10:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:10:25: #2 number of paired peaks: 1787 INFO @ Wed, 08 Dec 2021 19:10:25: start model_add_line... INFO @ Wed, 08 Dec 2021 19:10:25: start X-correlation... INFO @ Wed, 08 Dec 2021 19:10:25: end of X-cor INFO @ Wed, 08 Dec 2021 19:10:25: #2 finished! INFO @ Wed, 08 Dec 2021 19:10:25: #2 predicted fragment length is 254 bps INFO @ Wed, 08 Dec 2021 19:10:25: #2 alternative fragment length(s) may be 4,254 bps INFO @ Wed, 08 Dec 2021 19:10:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.05_model.r WARNING @ Wed, 08 Dec 2021 19:10:25: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:10:25: #2 You may need to consider one of the other alternative d(s): 4,254 WARNING @ Wed, 08 Dec 2021 19:10:25: #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 19:10:25: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:10:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:10:27: 12000000 INFO @ Wed, 08 Dec 2021 19:10:34: 14000000 INFO @ Wed, 08 Dec 2021 19:10:36: 13000000 INFO @ Wed, 08 Dec 2021 19:10:42: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:10:45: 15000000 INFO @ Wed, 08 Dec 2021 19:10:46: 14000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.05_summits.bed INFO @ Wed, 08 Dec 2021 19:10:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1969 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:10:55: 15000000 INFO @ Wed, 08 Dec 2021 19:10:56: 16000000 INFO @ Wed, 08 Dec 2021 19:11:04: 16000000 INFO @ Wed, 08 Dec 2021 19:11:07: 17000000 INFO @ Wed, 08 Dec 2021 19:11:14: 17000000 INFO @ Wed, 08 Dec 2021 19:11:19: 18000000 INFO @ Wed, 08 Dec 2021 19:11:23: 18000000 INFO @ Wed, 08 Dec 2021 19:11:28: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:11:28: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:11:28: #1 total tags in treatment: 6137879 INFO @ Wed, 08 Dec 2021 19:11:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:11:28: #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 19:11:28: #1 tags after filtering in treatment: 5714816 INFO @ Wed, 08 Dec 2021 19:11:28: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:11:28: #1 finished! INFO @ Wed, 08 Dec 2021 19:11:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:11:28: #2 number of paired peaks: 1787 INFO @ Wed, 08 Dec 2021 19:11:28: start model_add_line... INFO @ Wed, 08 Dec 2021 19:11:28: start X-correlation... INFO @ Wed, 08 Dec 2021 19:11:28: end of X-cor INFO @ Wed, 08 Dec 2021 19:11:28: #2 finished! INFO @ Wed, 08 Dec 2021 19:11:28: #2 predicted fragment length is 254 bps INFO @ Wed, 08 Dec 2021 19:11:28: #2 alternative fragment length(s) may be 4,254 bps INFO @ Wed, 08 Dec 2021 19:11:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.10_model.r WARNING @ Wed, 08 Dec 2021 19:11:28: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:11:28: #2 You may need to consider one of the other alternative d(s): 4,254 WARNING @ Wed, 08 Dec 2021 19:11:28: #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 19:11:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:11:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:11:30: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:11:30: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:11:30: #1 total tags in treatment: 6137879 INFO @ Wed, 08 Dec 2021 19:11:30: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:11:30: #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 19:11:30: #1 tags after filtering in treatment: 5714816 INFO @ Wed, 08 Dec 2021 19:11:30: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:11:30: #1 finished! INFO @ Wed, 08 Dec 2021 19:11:30: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:11:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:11:31: #2 number of paired peaks: 1787 INFO @ Wed, 08 Dec 2021 19:11:31: start model_add_line... INFO @ Wed, 08 Dec 2021 19:11:31: start X-correlation... INFO @ Wed, 08 Dec 2021 19:11:31: end of X-cor INFO @ Wed, 08 Dec 2021 19:11:31: #2 finished! INFO @ Wed, 08 Dec 2021 19:11:31: #2 predicted fragment length is 254 bps INFO @ Wed, 08 Dec 2021 19:11:31: #2 alternative fragment length(s) may be 4,254 bps INFO @ Wed, 08 Dec 2021 19:11:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.20_model.r WARNING @ Wed, 08 Dec 2021 19:11:31: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:11:31: #2 You may need to consider one of the other alternative d(s): 4,254 WARNING @ Wed, 08 Dec 2021 19:11:31: #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 19:11:31: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:11:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:11:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:11:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.10_summits.bed INFO @ Wed, 08 Dec 2021 19:11:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (866 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:11:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641180/SRX10641180.20_summits.bed INFO @ Wed, 08 Dec 2021 19:11:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (370 records, 4 fields): 2 millis CompletedMACS2peakCalling