Job ID = 12264832 SRX = SRX7687155 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26612955 spots for SRR11034898/SRR11034898.sra Written 26612955 spots for SRR11034898/SRR11034898.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265402 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:31:32 26612955 reads; of these: 26612955 (100.00%) were paired; of these: 4650751 (17.48%) aligned concordantly 0 times 19817290 (74.46%) aligned concordantly exactly 1 time 2144914 (8.06%) aligned concordantly >1 times ---- 4650751 pairs aligned concordantly 0 times; of these: 2629611 (56.54%) aligned discordantly 1 time ---- 2021140 pairs aligned 0 times concordantly or discordantly; of these: 4042280 mates make up the pairs; of these: 3251807 (80.44%) aligned 0 times 391612 (9.69%) aligned exactly 1 time 398861 (9.87%) aligned >1 times 93.89% overall alignment rate Time searching: 00:31:32 Overall time: 00:31:32 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 24 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] 13910837 / 24555817 = 0.5665 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:40:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.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 @ Sat, 03 Apr 2021 06:40:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:40:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:41:07: 1000000 INFO @ Sat, 03 Apr 2021 06:41:15: 2000000 INFO @ Sat, 03 Apr 2021 06:41:22: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.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 @ Sat, 03 Apr 2021 06:41:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:41:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:41:30: 4000000 INFO @ Sat, 03 Apr 2021 06:41:36: 1000000 INFO @ Sat, 03 Apr 2021 06:41:40: 5000000 INFO @ Sat, 03 Apr 2021 06:41:45: 2000000 INFO @ Sat, 03 Apr 2021 06:41:49: 6000000 INFO @ Sat, 03 Apr 2021 06:41:55: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.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 @ Sat, 03 Apr 2021 06:41:58: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:41:58: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:41:58: 7000000 INFO @ Sat, 03 Apr 2021 06:42:04: 4000000 INFO @ Sat, 03 Apr 2021 06:42:07: 8000000 INFO @ Sat, 03 Apr 2021 06:42:07: 1000000 INFO @ Sat, 03 Apr 2021 06:42:13: 5000000 INFO @ Sat, 03 Apr 2021 06:42:16: 9000000 INFO @ Sat, 03 Apr 2021 06:42:17: 2000000 INFO @ Sat, 03 Apr 2021 06:42:23: 6000000 INFO @ Sat, 03 Apr 2021 06:42:25: 10000000 INFO @ Sat, 03 Apr 2021 06:42:26: 3000000 INFO @ Sat, 03 Apr 2021 06:42:33: 7000000 INFO @ Sat, 03 Apr 2021 06:42:34: 11000000 INFO @ Sat, 03 Apr 2021 06:42:36: 4000000 INFO @ Sat, 03 Apr 2021 06:42:42: 8000000 INFO @ Sat, 03 Apr 2021 06:42:43: 12000000 INFO @ Sat, 03 Apr 2021 06:42:45: 5000000 INFO @ Sat, 03 Apr 2021 06:42:51: 9000000 INFO @ Sat, 03 Apr 2021 06:42:52: 13000000 INFO @ Sat, 03 Apr 2021 06:42:55: 6000000 INFO @ Sat, 03 Apr 2021 06:43:00: 10000000 INFO @ Sat, 03 Apr 2021 06:43:01: 14000000 INFO @ Sat, 03 Apr 2021 06:43:03: 7000000 INFO @ Sat, 03 Apr 2021 06:43:08: 11000000 INFO @ Sat, 03 Apr 2021 06:43:10: 15000000 INFO @ Sat, 03 Apr 2021 06:43:12: 8000000 INFO @ Sat, 03 Apr 2021 06:43:17: 12000000 INFO @ Sat, 03 Apr 2021 06:43:18: 16000000 INFO @ Sat, 03 Apr 2021 06:43:20: 9000000 INFO @ Sat, 03 Apr 2021 06:43:25: 13000000 INFO @ Sat, 03 Apr 2021 06:43:27: 17000000 INFO @ Sat, 03 Apr 2021 06:43:28: 10000000 INFO @ Sat, 03 Apr 2021 06:43:34: 14000000 INFO @ Sat, 03 Apr 2021 06:43:36: 11000000 INFO @ Sat, 03 Apr 2021 06:43:36: 18000000 INFO @ Sat, 03 Apr 2021 06:43:42: 15000000 INFO @ Sat, 03 Apr 2021 06:43:44: 12000000 INFO @ Sat, 03 Apr 2021 06:43:45: 19000000 INFO @ Sat, 03 Apr 2021 06:43:50: 16000000 INFO @ Sat, 03 Apr 2021 06:43:52: 13000000 INFO @ Sat, 03 Apr 2021 06:43:53: 20000000 INFO @ Sat, 03 Apr 2021 06:43:59: 17000000 INFO @ Sat, 03 Apr 2021 06:44:00: 14000000 INFO @ Sat, 03 Apr 2021 06:44:01: 21000000 INFO @ Sat, 03 Apr 2021 06:44:08: 15000000 INFO @ Sat, 03 Apr 2021 06:44:08: 18000000 INFO @ Sat, 03 Apr 2021 06:44:09: 22000000 INFO @ Sat, 03 Apr 2021 06:44:11: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:44:11: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:44:11: #1 total tags in treatment: 9379507 INFO @ Sat, 03 Apr 2021 06:44:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:44:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:44:11: #1 tags after filtering in treatment: 7067851 INFO @ Sat, 03 Apr 2021 06:44:11: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 06:44:11: #1 finished! INFO @ Sat, 03 Apr 2021 06:44:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:44:11: #2 number of paired peaks: 353 WARNING @ Sat, 03 Apr 2021 06:44:11: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Sat, 03 Apr 2021 06:44:11: start model_add_line... INFO @ Sat, 03 Apr 2021 06:44:12: start X-correlation... INFO @ Sat, 03 Apr 2021 06:44:12: end of X-cor INFO @ Sat, 03 Apr 2021 06:44:12: #2 finished! INFO @ Sat, 03 Apr 2021 06:44:12: #2 predicted fragment length is 122 bps INFO @ Sat, 03 Apr 2021 06:44:12: #2 alternative fragment length(s) may be 4,122,141,181 bps INFO @ Sat, 03 Apr 2021 06:44:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.05_model.r WARNING @ Sat, 03 Apr 2021 06:44:12: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:44:12: #2 You may need to consider one of the other alternative d(s): 4,122,141,181 WARNING @ Sat, 03 Apr 2021 06:44:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:44:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:44:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:44:16: 16000000 INFO @ Sat, 03 Apr 2021 06:44:16: 19000000 INFO @ Sat, 03 Apr 2021 06:44:24: 20000000 INFO @ Sat, 03 Apr 2021 06:44:24: 17000000 INFO @ Sat, 03 Apr 2021 06:44:31: 21000000 INFO @ Sat, 03 Apr 2021 06:44:33: 18000000 INFO @ Sat, 03 Apr 2021 06:44:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:44:39: 22000000 INFO @ Sat, 03 Apr 2021 06:44:40: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:44:40: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:44:40: #1 total tags in treatment: 9379507 INFO @ Sat, 03 Apr 2021 06:44:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:44:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:44:40: #1 tags after filtering in treatment: 7067851 INFO @ Sat, 03 Apr 2021 06:44:40: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 06:44:40: #1 finished! INFO @ Sat, 03 Apr 2021 06:44:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:44:41: #2 number of paired peaks: 353 WARNING @ Sat, 03 Apr 2021 06:44:41: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Sat, 03 Apr 2021 06:44:41: start model_add_line... INFO @ Sat, 03 Apr 2021 06:44:41: start X-correlation... INFO @ Sat, 03 Apr 2021 06:44:41: end of X-cor INFO @ Sat, 03 Apr 2021 06:44:41: #2 finished! INFO @ Sat, 03 Apr 2021 06:44:41: #2 predicted fragment length is 122 bps INFO @ Sat, 03 Apr 2021 06:44:41: #2 alternative fragment length(s) may be 4,122,141,181 bps INFO @ Sat, 03 Apr 2021 06:44:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.10_model.r WARNING @ Sat, 03 Apr 2021 06:44:41: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:44:41: #2 You may need to consider one of the other alternative d(s): 4,122,141,181 WARNING @ Sat, 03 Apr 2021 06:44:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:44:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:44:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:44:42: 19000000 INFO @ Sat, 03 Apr 2021 06:44:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.05_summits.bed INFO @ Sat, 03 Apr 2021 06:44:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (788 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:44:51: 20000000 INFO @ Sat, 03 Apr 2021 06:45:00: 21000000 INFO @ Sat, 03 Apr 2021 06:45:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:45:09: 22000000 INFO @ Sat, 03 Apr 2021 06:45:10: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:45:10: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:45:10: #1 total tags in treatment: 9379507 INFO @ Sat, 03 Apr 2021 06:45:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:45:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:45:10: #1 tags after filtering in treatment: 7067851 INFO @ Sat, 03 Apr 2021 06:45:10: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 06:45:10: #1 finished! INFO @ Sat, 03 Apr 2021 06:45:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:45:11: #2 number of paired peaks: 353 WARNING @ Sat, 03 Apr 2021 06:45:11: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Sat, 03 Apr 2021 06:45:11: start model_add_line... INFO @ Sat, 03 Apr 2021 06:45:11: start X-correlation... INFO @ Sat, 03 Apr 2021 06:45:11: end of X-cor INFO @ Sat, 03 Apr 2021 06:45:11: #2 finished! INFO @ Sat, 03 Apr 2021 06:45:11: #2 predicted fragment length is 122 bps INFO @ Sat, 03 Apr 2021 06:45:11: #2 alternative fragment length(s) may be 4,122,141,181 bps INFO @ Sat, 03 Apr 2021 06:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.20_model.r WARNING @ Sat, 03 Apr 2021 06:45:11: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:45:11: #2 You may need to consider one of the other alternative d(s): 4,122,141,181 WARNING @ Sat, 03 Apr 2021 06:45:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:45:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:45:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:45:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:45:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.10_summits.bed INFO @ Sat, 03 Apr 2021 06:45:16: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (368 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:45:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:45:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:45:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:45:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687155/SRX7687155.20_summits.bed INFO @ Sat, 03 Apr 2021 06:45:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (148 records, 4 fields): 2 millis CompletedMACS2peakCalling