Job ID = 14159209 SRX = SRX10641196 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: 00:35:35 21102173 reads; of these: 21102173 (100.00%) were paired; of these: 13230937 (62.70%) aligned concordantly 0 times 4715050 (22.34%) aligned concordantly exactly 1 time 3156186 (14.96%) aligned concordantly >1 times ---- 13230937 pairs aligned concordantly 0 times; of these: 1926038 (14.56%) aligned discordantly 1 time ---- 11304899 pairs aligned 0 times concordantly or discordantly; of these: 22609798 mates make up the pairs; of these: 21614975 (95.60%) aligned 0 times 482161 (2.13%) aligned exactly 1 time 512662 (2.27%) aligned >1 times 48.78% overall alignment rate Time searching: 00:35:35 Overall time: 00:35:35 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] 2225700 / 9750563 = 0.2283 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 20:58:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.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 20:58:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:58:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:58:21: 1000000 INFO @ Wed, 08 Dec 2021 20:58:29: 2000000 INFO @ Wed, 08 Dec 2021 20:58:37: 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 20:58:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.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 20:58:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:58:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:58:45: 4000000 INFO @ Wed, 08 Dec 2021 20:58:50: 1000000 INFO @ Wed, 08 Dec 2021 20:58:53: 5000000 INFO @ Wed, 08 Dec 2021 20:58:57: 2000000 INFO @ Wed, 08 Dec 2021 20:59:01: 6000000 INFO @ Wed, 08 Dec 2021 20:59:04: 3000000 INFO @ Wed, 08 Dec 2021 20:59:09: 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 20:59:12: 4000000 INFO @ Wed, 08 Dec 2021 20:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.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 20:59:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:59:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:59:18: 8000000 INFO @ Wed, 08 Dec 2021 20:59:19: 5000000 INFO @ Wed, 08 Dec 2021 20:59:21: 1000000 INFO @ Wed, 08 Dec 2021 20:59:26: 9000000 INFO @ Wed, 08 Dec 2021 20:59:26: 6000000 INFO @ Wed, 08 Dec 2021 20:59:30: 2000000 INFO @ Wed, 08 Dec 2021 20:59:33: 7000000 INFO @ Wed, 08 Dec 2021 20:59:34: 10000000 INFO @ Wed, 08 Dec 2021 20:59:38: 3000000 INFO @ Wed, 08 Dec 2021 20:59:41: 8000000 INFO @ Wed, 08 Dec 2021 20:59:42: 11000000 INFO @ Wed, 08 Dec 2021 20:59:46: 4000000 INFO @ Wed, 08 Dec 2021 20:59:48: 9000000 INFO @ Wed, 08 Dec 2021 20:59:51: 12000000 INFO @ Wed, 08 Dec 2021 20:59:55: 5000000 INFO @ Wed, 08 Dec 2021 20:59:55: 10000000 INFO @ Wed, 08 Dec 2021 20:59:59: 13000000 INFO @ Wed, 08 Dec 2021 21:00:02: 11000000 INFO @ Wed, 08 Dec 2021 21:00:03: 6000000 INFO @ Wed, 08 Dec 2021 21:00:07: 14000000 INFO @ Wed, 08 Dec 2021 21:00:10: 12000000 INFO @ Wed, 08 Dec 2021 21:00:11: 7000000 INFO @ Wed, 08 Dec 2021 21:00:15: 15000000 INFO @ Wed, 08 Dec 2021 21:00:17: 13000000 INFO @ Wed, 08 Dec 2021 21:00:19: 8000000 INFO @ Wed, 08 Dec 2021 21:00:23: 16000000 INFO @ Wed, 08 Dec 2021 21:00:24: 14000000 INFO @ Wed, 08 Dec 2021 21:00:25: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 21:00:25: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 21:00:25: #1 total tags in treatment: 5873671 INFO @ Wed, 08 Dec 2021 21:00:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:00:25: #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 21:00:25: #1 tags after filtering in treatment: 4470400 INFO @ Wed, 08 Dec 2021 21:00:25: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 21:00:25: #1 finished! INFO @ Wed, 08 Dec 2021 21:00:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:00:25: #2 number of paired peaks: 1025 INFO @ Wed, 08 Dec 2021 21:00:25: start model_add_line... INFO @ Wed, 08 Dec 2021 21:00:25: start X-correlation... INFO @ Wed, 08 Dec 2021 21:00:25: end of X-cor INFO @ Wed, 08 Dec 2021 21:00:25: #2 finished! INFO @ Wed, 08 Dec 2021 21:00:25: #2 predicted fragment length is 273 bps INFO @ Wed, 08 Dec 2021 21:00:25: #2 alternative fragment length(s) may be 273 bps INFO @ Wed, 08 Dec 2021 21:00:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.05_model.r WARNING @ Wed, 08 Dec 2021 21:00:25: #2 Since the d (273) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:00:25: #2 You may need to consider one of the other alternative d(s): 273 WARNING @ Wed, 08 Dec 2021 21:00:25: #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 21:00:25: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:00:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:00:28: 9000000 INFO @ Wed, 08 Dec 2021 21:00:31: 15000000 INFO @ Wed, 08 Dec 2021 21:00:36: 10000000 INFO @ Wed, 08 Dec 2021 21:00:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:00:39: 16000000 INFO @ Wed, 08 Dec 2021 21:00:40: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 21:00:40: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 21:00:40: #1 total tags in treatment: 5873671 INFO @ Wed, 08 Dec 2021 21:00:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:00:40: #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 21:00:40: #1 tags after filtering in treatment: 4470400 INFO @ Wed, 08 Dec 2021 21:00:40: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 21:00:40: #1 finished! INFO @ Wed, 08 Dec 2021 21:00:40: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:00:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:00:40: #2 number of paired peaks: 1025 INFO @ Wed, 08 Dec 2021 21:00:40: start model_add_line... BedGraph に変換しました。 INFO @ Wed, 08 Dec 2021 21:00:40: start X-correlation... BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:00:40: end of X-cor INFO @ Wed, 08 Dec 2021 21:00:40: #2 finished! INFO @ Wed, 08 Dec 2021 21:00:40: #2 predicted fragment length is 273 bps INFO @ Wed, 08 Dec 2021 21:00:40: #2 alternative fragment length(s) may be 273 bps INFO @ Wed, 08 Dec 2021 21:00:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.10_model.r WARNING @ Wed, 08 Dec 2021 21:00:40: #2 Since the d (273) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:00:40: #2 You may need to consider one of the other alternative d(s): 273 WARNING @ Wed, 08 Dec 2021 21:00:40: #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 21:00:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:00:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.05_summits.bed INFO @ Wed, 08 Dec 2021 21:00:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1312 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:00:44: 11000000 INFO @ Wed, 08 Dec 2021 21:00:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:00:52: 12000000 INFO @ Wed, 08 Dec 2021 21:00:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:00:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:00:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.10_summits.bed INFO @ Wed, 08 Dec 2021 21:00:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (754 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:01:00: 13000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:01:08: 14000000 INFO @ Wed, 08 Dec 2021 21:01:17: 15000000 INFO @ Wed, 08 Dec 2021 21:01:25: 16000000 INFO @ Wed, 08 Dec 2021 21:01:26: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 21:01:26: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 21:01:26: #1 total tags in treatment: 5873671 INFO @ Wed, 08 Dec 2021 21:01:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:01:26: #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 21:01:26: #1 tags after filtering in treatment: 4470400 INFO @ Wed, 08 Dec 2021 21:01:26: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 21:01:26: #1 finished! INFO @ Wed, 08 Dec 2021 21:01:26: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:01:26: #2 number of paired peaks: 1025 INFO @ Wed, 08 Dec 2021 21:01:26: start model_add_line... INFO @ Wed, 08 Dec 2021 21:01:26: start X-correlation... INFO @ Wed, 08 Dec 2021 21:01:26: end of X-cor INFO @ Wed, 08 Dec 2021 21:01:26: #2 finished! INFO @ Wed, 08 Dec 2021 21:01:26: #2 predicted fragment length is 273 bps INFO @ Wed, 08 Dec 2021 21:01:26: #2 alternative fragment length(s) may be 273 bps INFO @ Wed, 08 Dec 2021 21:01:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.20_model.r WARNING @ Wed, 08 Dec 2021 21:01:26: #2 Since the d (273) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:01:26: #2 You may need to consider one of the other alternative d(s): 273 WARNING @ Wed, 08 Dec 2021 21:01:26: #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 21:01:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:01:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:01:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641196/SRX10641196.20_summits.bed INFO @ Wed, 08 Dec 2021 21:01:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (493 records, 4 fields): 2 millis CompletedMACS2peakCalling