Job ID = 14158982 SRX = SRX10641178 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: 00:00:01 Multiseed full-index search: 00:34:18 21556117 reads; of these: 21556117 (100.00%) were paired; of these: 15270002 (70.84%) aligned concordantly 0 times 5599629 (25.98%) aligned concordantly exactly 1 time 686486 (3.18%) aligned concordantly >1 times ---- 15270002 pairs aligned concordantly 0 times; of these: 2505812 (16.41%) aligned discordantly 1 time ---- 12764190 pairs aligned 0 times concordantly or discordantly; of these: 25528380 mates make up the pairs; of these: 24434745 (95.72%) aligned 0 times 574465 (2.25%) aligned exactly 1 time 519170 (2.03%) aligned >1 times 43.32% overall alignment rate Time searching: 00:34:19 Overall time: 00:34:19 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] 1145410 / 8770190 = 0.1306 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 19:18:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.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 19:18:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:18:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:18:41: 1000000 INFO @ Wed, 08 Dec 2021 19:18:53: 2000000 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 19:18:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.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 19:18:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:18:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:19:06: 3000000 INFO @ Wed, 08 Dec 2021 19:19:13: 1000000 INFO @ Wed, 08 Dec 2021 19:19:18: 4000000 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 19:19:27: 2000000 INFO @ Wed, 08 Dec 2021 19:19:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.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 19:19:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:19:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:19:30: 5000000 INFO @ Wed, 08 Dec 2021 19:19:42: 3000000 INFO @ Wed, 08 Dec 2021 19:19:43: 1000000 INFO @ Wed, 08 Dec 2021 19:19:43: 6000000 INFO @ Wed, 08 Dec 2021 19:19:56: 7000000 INFO @ Wed, 08 Dec 2021 19:19:57: 4000000 INFO @ Wed, 08 Dec 2021 19:19:58: 2000000 INFO @ Wed, 08 Dec 2021 19:20:09: 8000000 INFO @ Wed, 08 Dec 2021 19:20:11: 5000000 INFO @ Wed, 08 Dec 2021 19:20:13: 3000000 INFO @ Wed, 08 Dec 2021 19:20:22: 9000000 INFO @ Wed, 08 Dec 2021 19:20:26: 6000000 INFO @ Wed, 08 Dec 2021 19:20:28: 4000000 INFO @ Wed, 08 Dec 2021 19:20:35: 10000000 INFO @ Wed, 08 Dec 2021 19:20:40: 7000000 INFO @ Wed, 08 Dec 2021 19:20:43: 5000000 INFO @ Wed, 08 Dec 2021 19:20:47: 11000000 INFO @ Wed, 08 Dec 2021 19:20:55: 8000000 INFO @ Wed, 08 Dec 2021 19:20:59: 6000000 INFO @ Wed, 08 Dec 2021 19:21:00: 12000000 INFO @ Wed, 08 Dec 2021 19:21:10: 9000000 INFO @ Wed, 08 Dec 2021 19:21:13: 13000000 INFO @ Wed, 08 Dec 2021 19:21:14: 7000000 INFO @ Wed, 08 Dec 2021 19:21:26: 14000000 INFO @ Wed, 08 Dec 2021 19:21:26: 10000000 INFO @ Wed, 08 Dec 2021 19:21:30: 8000000 INFO @ Wed, 08 Dec 2021 19:21:39: 15000000 INFO @ Wed, 08 Dec 2021 19:21:41: 11000000 INFO @ Wed, 08 Dec 2021 19:21:46: 9000000 INFO @ Wed, 08 Dec 2021 19:21:52: 16000000 INFO @ Wed, 08 Dec 2021 19:21:56: 12000000 INFO @ Wed, 08 Dec 2021 19:21:57: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:21:57: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:21:57: #1 total tags in treatment: 5395321 INFO @ Wed, 08 Dec 2021 19:21:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:21:57: #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 19:21:57: #1 tags after filtering in treatment: 5011430 INFO @ Wed, 08 Dec 2021 19:21:57: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:21:57: #1 finished! INFO @ Wed, 08 Dec 2021 19:21:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:21:57: #2 number of paired peaks: 1957 INFO @ Wed, 08 Dec 2021 19:21:57: start model_add_line... INFO @ Wed, 08 Dec 2021 19:21:58: start X-correlation... INFO @ Wed, 08 Dec 2021 19:21:58: end of X-cor INFO @ Wed, 08 Dec 2021 19:21:58: #2 finished! INFO @ Wed, 08 Dec 2021 19:21:58: #2 predicted fragment length is 263 bps INFO @ Wed, 08 Dec 2021 19:21:58: #2 alternative fragment length(s) may be 263 bps INFO @ Wed, 08 Dec 2021 19:21:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.05_model.r WARNING @ Wed, 08 Dec 2021 19:21:58: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:21:58: #2 You may need to consider one of the other alternative d(s): 263 WARNING @ Wed, 08 Dec 2021 19:21:58: #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 19:21:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:21:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:22:01: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:22:13: 13000000 INFO @ Wed, 08 Dec 2021 19:22:17: 11000000 INFO @ Wed, 08 Dec 2021 19:22:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:22:28: 14000000 INFO @ Wed, 08 Dec 2021 19:22:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:22:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:22:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.05_summits.bed INFO @ Wed, 08 Dec 2021 19:22:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2462 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:22:32: 12000000 INFO @ Wed, 08 Dec 2021 19:22:43: 15000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:22:48: 13000000 INFO @ Wed, 08 Dec 2021 19:22:59: 16000000 INFO @ Wed, 08 Dec 2021 19:23:03: 14000000 INFO @ Wed, 08 Dec 2021 19:23:05: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:23:05: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:23:05: #1 total tags in treatment: 5395321 INFO @ Wed, 08 Dec 2021 19:23:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:23:05: #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 19:23:05: #1 tags after filtering in treatment: 5011430 INFO @ Wed, 08 Dec 2021 19:23:05: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:23:05: #1 finished! INFO @ Wed, 08 Dec 2021 19:23:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:23:06: #2 number of paired peaks: 1957 INFO @ Wed, 08 Dec 2021 19:23:06: start model_add_line... INFO @ Wed, 08 Dec 2021 19:23:06: start X-correlation... INFO @ Wed, 08 Dec 2021 19:23:06: end of X-cor INFO @ Wed, 08 Dec 2021 19:23:06: #2 finished! INFO @ Wed, 08 Dec 2021 19:23:06: #2 predicted fragment length is 263 bps INFO @ Wed, 08 Dec 2021 19:23:06: #2 alternative fragment length(s) may be 263 bps INFO @ Wed, 08 Dec 2021 19:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.10_model.r WARNING @ Wed, 08 Dec 2021 19:23:06: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:23:06: #2 You may need to consider one of the other alternative d(s): 263 WARNING @ Wed, 08 Dec 2021 19:23:06: #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 19:23:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:23:18: 15000000 INFO @ Wed, 08 Dec 2021 19:23:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:23:33: 16000000 INFO @ Wed, 08 Dec 2021 19:23:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:23:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:23:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.10_summits.bed INFO @ Wed, 08 Dec 2021 19:23:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1100 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:23:39: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:23:39: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:23:39: #1 total tags in treatment: 5395321 INFO @ Wed, 08 Dec 2021 19:23:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:23:39: #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 19:23:39: #1 tags after filtering in treatment: 5011430 INFO @ Wed, 08 Dec 2021 19:23:39: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:23:39: #1 finished! INFO @ Wed, 08 Dec 2021 19:23:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:23:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:23:39: #2 number of paired peaks: 1957 INFO @ Wed, 08 Dec 2021 19:23:39: start model_add_line... INFO @ Wed, 08 Dec 2021 19:23:39: start X-correlation... INFO @ Wed, 08 Dec 2021 19:23:39: end of X-cor INFO @ Wed, 08 Dec 2021 19:23:39: #2 finished! INFO @ Wed, 08 Dec 2021 19:23:39: #2 predicted fragment length is 263 bps INFO @ Wed, 08 Dec 2021 19:23:39: #2 alternative fragment length(s) may be 263 bps INFO @ Wed, 08 Dec 2021 19:23:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.20_model.r WARNING @ Wed, 08 Dec 2021 19:23:39: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:23:39: #2 You may need to consider one of the other alternative d(s): 263 WARNING @ Wed, 08 Dec 2021 19:23:39: #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 19:23:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:23:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:24:01: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:24:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:24:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:24:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641178/SRX10641178.20_summits.bed INFO @ Wed, 08 Dec 2021 19:24:10: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (468 records, 4 fields): 3 millis CompletedMACS2peakCalling