Job ID = 14159198 SRX = SRX10641192 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: 00:33:39 22401560 reads; of these: 22401560 (100.00%) were paired; of these: 14531279 (64.87%) aligned concordantly 0 times 4842475 (21.62%) aligned concordantly exactly 1 time 3027806 (13.52%) aligned concordantly >1 times ---- 14531279 pairs aligned concordantly 0 times; of these: 1737169 (11.95%) aligned discordantly 1 time ---- 12794110 pairs aligned 0 times concordantly or discordantly; of these: 25588220 mates make up the pairs; of these: 24643662 (96.31%) aligned 0 times 473226 (1.85%) aligned exactly 1 time 471332 (1.84%) aligned >1 times 45.00% overall alignment rate Time searching: 00:33:39 Overall time: 00:33:39 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] 2156909 / 9566958 = 0.2255 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 20:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.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 20:53:00: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:53:00: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:53:07: 1000000 INFO @ Wed, 08 Dec 2021 20:53:14: 2000000 INFO @ Wed, 08 Dec 2021 20:53:21: 3000000 INFO @ Wed, 08 Dec 2021 20:53:27: 4000000 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 20:53:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.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 20:53:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:53:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:53:35: 5000000 INFO @ Wed, 08 Dec 2021 20:53:38: 1000000 INFO @ Wed, 08 Dec 2021 20:53:42: 6000000 INFO @ Wed, 08 Dec 2021 20:53:47: 2000000 INFO @ Wed, 08 Dec 2021 20:53:50: 7000000 INFO @ Wed, 08 Dec 2021 20:53:55: 3000000 INFO @ Wed, 08 Dec 2021 20:53:58: 8000000 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 20:54:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.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 20:54:00: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:54:00: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:54:04: 4000000 INFO @ Wed, 08 Dec 2021 20:54:05: 9000000 INFO @ Wed, 08 Dec 2021 20:54:07: 1000000 INFO @ Wed, 08 Dec 2021 20:54:12: 5000000 INFO @ Wed, 08 Dec 2021 20:54:13: 10000000 INFO @ Wed, 08 Dec 2021 20:54:15: 2000000 INFO @ Wed, 08 Dec 2021 20:54:20: 11000000 INFO @ Wed, 08 Dec 2021 20:54:21: 6000000 INFO @ Wed, 08 Dec 2021 20:54:22: 3000000 INFO @ Wed, 08 Dec 2021 20:54:28: 12000000 INFO @ Wed, 08 Dec 2021 20:54:29: 7000000 INFO @ Wed, 08 Dec 2021 20:54:30: 4000000 INFO @ Wed, 08 Dec 2021 20:54:36: 13000000 INFO @ Wed, 08 Dec 2021 20:54:38: 5000000 INFO @ Wed, 08 Dec 2021 20:54:38: 8000000 INFO @ Wed, 08 Dec 2021 20:54:43: 14000000 INFO @ Wed, 08 Dec 2021 20:54:45: 6000000 INFO @ Wed, 08 Dec 2021 20:54:46: 9000000 INFO @ Wed, 08 Dec 2021 20:54:51: 15000000 INFO @ Wed, 08 Dec 2021 20:54:53: 7000000 INFO @ Wed, 08 Dec 2021 20:54:55: 10000000 INFO @ Wed, 08 Dec 2021 20:54:57: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:54:57: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:54:57: #1 total tags in treatment: 5926581 INFO @ Wed, 08 Dec 2021 20:54:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:54:57: #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 20:54:57: #1 tags after filtering in treatment: 4466666 INFO @ Wed, 08 Dec 2021 20:54:57: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 08 Dec 2021 20:54:57: #1 finished! INFO @ Wed, 08 Dec 2021 20:54:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:54:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:54:58: #2 number of paired peaks: 1415 INFO @ Wed, 08 Dec 2021 20:54:58: start model_add_line... INFO @ Wed, 08 Dec 2021 20:54:58: start X-correlation... INFO @ Wed, 08 Dec 2021 20:54:58: end of X-cor INFO @ Wed, 08 Dec 2021 20:54:58: #2 finished! INFO @ Wed, 08 Dec 2021 20:54:58: #2 predicted fragment length is 268 bps INFO @ Wed, 08 Dec 2021 20:54:58: #2 alternative fragment length(s) may be 268 bps INFO @ Wed, 08 Dec 2021 20:54:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.05_model.r WARNING @ Wed, 08 Dec 2021 20:54:58: #2 Since the d (268) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:54:58: #2 You may need to consider one of the other alternative d(s): 268 WARNING @ Wed, 08 Dec 2021 20:54:58: #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 20:54:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:54:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:55:00: 8000000 INFO @ Wed, 08 Dec 2021 20:55:03: 11000000 INFO @ Wed, 08 Dec 2021 20:55:08: 9000000 INFO @ Wed, 08 Dec 2021 20:55:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:55:12: 12000000 INFO @ Wed, 08 Dec 2021 20:55:15: 10000000 INFO @ Wed, 08 Dec 2021 20:55:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:55:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:55:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.05_summits.bed INFO @ Wed, 08 Dec 2021 20:55:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2411 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:55:20: 13000000 INFO @ Wed, 08 Dec 2021 20:55:23: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:55:29: 14000000 INFO @ Wed, 08 Dec 2021 20:55:30: 12000000 INFO @ Wed, 08 Dec 2021 20:55:38: 13000000 INFO @ Wed, 08 Dec 2021 20:55:38: 15000000 INFO @ Wed, 08 Dec 2021 20:55:45: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:55:45: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:55:45: #1 total tags in treatment: 5926581 INFO @ Wed, 08 Dec 2021 20:55:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:55:45: #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 20:55:45: #1 tags after filtering in treatment: 4466666 INFO @ Wed, 08 Dec 2021 20:55:45: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 08 Dec 2021 20:55:45: #1 finished! INFO @ Wed, 08 Dec 2021 20:55:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:55:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:55:45: 14000000 INFO @ Wed, 08 Dec 2021 20:55:45: #2 number of paired peaks: 1415 INFO @ Wed, 08 Dec 2021 20:55:45: start model_add_line... INFO @ Wed, 08 Dec 2021 20:55:45: start X-correlation... INFO @ Wed, 08 Dec 2021 20:55:45: end of X-cor INFO @ Wed, 08 Dec 2021 20:55:45: #2 finished! INFO @ Wed, 08 Dec 2021 20:55:45: #2 predicted fragment length is 268 bps INFO @ Wed, 08 Dec 2021 20:55:45: #2 alternative fragment length(s) may be 268 bps INFO @ Wed, 08 Dec 2021 20:55:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.10_model.r WARNING @ Wed, 08 Dec 2021 20:55:45: #2 Since the d (268) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:55:45: #2 You may need to consider one of the other alternative d(s): 268 WARNING @ Wed, 08 Dec 2021 20:55:45: #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 20:55:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:55:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:55:52: 15000000 INFO @ Wed, 08 Dec 2021 20:55:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:55:58: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:55:58: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:55:58: #1 total tags in treatment: 5926581 INFO @ Wed, 08 Dec 2021 20:55:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:55:58: #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 20:55:58: #1 tags after filtering in treatment: 4466666 INFO @ Wed, 08 Dec 2021 20:55:58: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 08 Dec 2021 20:55:58: #1 finished! INFO @ Wed, 08 Dec 2021 20:55:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:55:59: #2 number of paired peaks: 1415 INFO @ Wed, 08 Dec 2021 20:55:59: start model_add_line... INFO @ Wed, 08 Dec 2021 20:55:59: start X-correlation... INFO @ Wed, 08 Dec 2021 20:55:59: end of X-cor INFO @ Wed, 08 Dec 2021 20:55:59: #2 finished! INFO @ Wed, 08 Dec 2021 20:55:59: #2 predicted fragment length is 268 bps INFO @ Wed, 08 Dec 2021 20:55:59: #2 alternative fragment length(s) may be 268 bps INFO @ Wed, 08 Dec 2021 20:55:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.20_model.r WARNING @ Wed, 08 Dec 2021 20:55:59: #2 Since the d (268) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:55:59: #2 You may need to consider one of the other alternative d(s): 268 WARNING @ Wed, 08 Dec 2021 20:55:59: #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 20:55:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:56:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:56:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:56:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.10_summits.bed INFO @ Wed, 08 Dec 2021 20:56:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1322 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:56:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641192/SRX10641192.20_summits.bed INFO @ Wed, 08 Dec 2021 20:56:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (742 records, 4 fields): 2 millis CompletedMACS2peakCalling