Job ID = 14160413 SRX = SRX9567192 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16947048 spots for SRR13125167/SRR13125167.sra Written 16947048 spots for SRR13125167/SRR13125167.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160615 ("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: 00:33:28 16947048 reads; of these: 16947048 (100.00%) were paired; of these: 7569150 (44.66%) aligned concordantly 0 times 8396410 (49.54%) aligned concordantly exactly 1 time 981488 (5.79%) aligned concordantly >1 times ---- 7569150 pairs aligned concordantly 0 times; of these: 5787643 (76.46%) aligned discordantly 1 time ---- 1781507 pairs aligned 0 times concordantly or discordantly; of these: 3563014 mates make up the pairs; of these: 1204441 (33.80%) aligned 0 times 1118043 (31.38%) aligned exactly 1 time 1240530 (34.82%) aligned >1 times 96.45% overall alignment rate Time searching: 00:33:28 Overall time: 00:33:28 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] 9337649 / 15159334 = 0.6160 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 @ Thu, 09 Dec 2021 03:00:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.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 @ Thu, 09 Dec 2021 03:00:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:00:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:00:47: 1000000 INFO @ Thu, 09 Dec 2021 03:00:53: 2000000 INFO @ Thu, 09 Dec 2021 03:00:59: 3000000 INFO @ Thu, 09 Dec 2021 03:01:05: 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 @ Thu, 09 Dec 2021 03:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.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 @ Thu, 09 Dec 2021 03:01:11: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:01:11: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:01:11: 5000000 INFO @ Thu, 09 Dec 2021 03:01:18: 6000000 INFO @ Thu, 09 Dec 2021 03:01:18: 1000000 INFO @ Thu, 09 Dec 2021 03:01:24: 7000000 INFO @ Thu, 09 Dec 2021 03:01:24: 2000000 INFO @ Thu, 09 Dec 2021 03:01:31: 3000000 INFO @ Thu, 09 Dec 2021 03:01:31: 8000000 INFO @ Thu, 09 Dec 2021 03:01:37: 4000000 INFO @ Thu, 09 Dec 2021 03:01:37: 9000000 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 @ Thu, 09 Dec 2021 03:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.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 @ Thu, 09 Dec 2021 03:01:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:01:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:01:43: 5000000 INFO @ Thu, 09 Dec 2021 03:01:44: 10000000 INFO @ Thu, 09 Dec 2021 03:01:48: 1000000 INFO @ Thu, 09 Dec 2021 03:01:50: 6000000 INFO @ Thu, 09 Dec 2021 03:01:50: 11000000 INFO @ Thu, 09 Dec 2021 03:01:54: 2000000 INFO @ Thu, 09 Dec 2021 03:01:56: 7000000 INFO @ Thu, 09 Dec 2021 03:01:57: 12000000 INFO @ Thu, 09 Dec 2021 03:02:01: 3000000 INFO @ Thu, 09 Dec 2021 03:02:03: 8000000 INFO @ Thu, 09 Dec 2021 03:02:03: 13000000 INFO @ Thu, 09 Dec 2021 03:02:07: 4000000 INFO @ Thu, 09 Dec 2021 03:02:09: 9000000 INFO @ Thu, 09 Dec 2021 03:02:10: 14000000 INFO @ Thu, 09 Dec 2021 03:02:10: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:02:10: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:02:10: #1 total tags in treatment: 3589965 INFO @ Thu, 09 Dec 2021 03:02:10: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:02:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:02:10: #1 tags after filtering in treatment: 3383966 INFO @ Thu, 09 Dec 2021 03:02:10: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 03:02:10: #1 finished! INFO @ Thu, 09 Dec 2021 03:02:10: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:02:10: #2 number of paired peaks: 2124 INFO @ Thu, 09 Dec 2021 03:02:10: start model_add_line... INFO @ Thu, 09 Dec 2021 03:02:10: start X-correlation... INFO @ Thu, 09 Dec 2021 03:02:10: end of X-cor INFO @ Thu, 09 Dec 2021 03:02:10: #2 finished! INFO @ Thu, 09 Dec 2021 03:02:10: #2 predicted fragment length is 283 bps INFO @ Thu, 09 Dec 2021 03:02:10: #2 alternative fragment length(s) may be 283 bps INFO @ Thu, 09 Dec 2021 03:02:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.05_model.r WARNING @ Thu, 09 Dec 2021 03:02:10: #2 Since the d (283) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:02:10: #2 You may need to consider one of the other alternative d(s): 283 WARNING @ Thu, 09 Dec 2021 03:02:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:02:10: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:02:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:02:14: 5000000 INFO @ Thu, 09 Dec 2021 03:02:16: 10000000 INFO @ Thu, 09 Dec 2021 03:02:19: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:02:20: 6000000 INFO @ Thu, 09 Dec 2021 03:02:22: 11000000 INFO @ Thu, 09 Dec 2021 03:02:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:02:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:02:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.05_summits.bed INFO @ Thu, 09 Dec 2021 03:02:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2231 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:02:26: 7000000 INFO @ Thu, 09 Dec 2021 03:02:29: 12000000 INFO @ Thu, 09 Dec 2021 03:02:33: 8000000 INFO @ Thu, 09 Dec 2021 03:02:36: 13000000 INFO @ Thu, 09 Dec 2021 03:02:39: 9000000 INFO @ Thu, 09 Dec 2021 03:02:42: 14000000 INFO @ Thu, 09 Dec 2021 03:02:42: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:02:42: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:02:42: #1 total tags in treatment: 3589965 INFO @ Thu, 09 Dec 2021 03:02:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:02:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:02:42: #1 tags after filtering in treatment: 3383966 INFO @ Thu, 09 Dec 2021 03:02:42: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 03:02:42: #1 finished! INFO @ Thu, 09 Dec 2021 03:02:42: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:02:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:02:43: #2 number of paired peaks: 2124 INFO @ Thu, 09 Dec 2021 03:02:43: start model_add_line... INFO @ Thu, 09 Dec 2021 03:02:43: start X-correlation... INFO @ Thu, 09 Dec 2021 03:02:43: end of X-cor INFO @ Thu, 09 Dec 2021 03:02:43: #2 finished! INFO @ Thu, 09 Dec 2021 03:02:43: #2 predicted fragment length is 283 bps INFO @ Thu, 09 Dec 2021 03:02:43: #2 alternative fragment length(s) may be 283 bps INFO @ Thu, 09 Dec 2021 03:02:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.10_model.r WARNING @ Thu, 09 Dec 2021 03:02:43: #2 Since the d (283) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:02:43: #2 You may need to consider one of the other alternative d(s): 283 WARNING @ Thu, 09 Dec 2021 03:02:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:02:43: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:02:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:02:46: 10000000 INFO @ Thu, 09 Dec 2021 03:02:52: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:02:52: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:02:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:02:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:02:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.10_summits.bed INFO @ Thu, 09 Dec 2021 03:02:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1149 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:02:58: 12000000 INFO @ Thu, 09 Dec 2021 03:03:04: 13000000 INFO @ Thu, 09 Dec 2021 03:03:10: 14000000 INFO @ Thu, 09 Dec 2021 03:03:10: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:03:10: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:03:10: #1 total tags in treatment: 3589965 INFO @ Thu, 09 Dec 2021 03:03:10: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:03:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:03:10: #1 tags after filtering in treatment: 3383966 INFO @ Thu, 09 Dec 2021 03:03:10: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 03:03:10: #1 finished! INFO @ Thu, 09 Dec 2021 03:03:10: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:03:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:03:10: #2 number of paired peaks: 2124 INFO @ Thu, 09 Dec 2021 03:03:10: start model_add_line... INFO @ Thu, 09 Dec 2021 03:03:11: start X-correlation... INFO @ Thu, 09 Dec 2021 03:03:11: end of X-cor INFO @ Thu, 09 Dec 2021 03:03:11: #2 finished! INFO @ Thu, 09 Dec 2021 03:03:11: #2 predicted fragment length is 283 bps INFO @ Thu, 09 Dec 2021 03:03:11: #2 alternative fragment length(s) may be 283 bps INFO @ Thu, 09 Dec 2021 03:03:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.20_model.r WARNING @ Thu, 09 Dec 2021 03:03:11: #2 Since the d (283) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:03:11: #2 You may need to consider one of the other alternative d(s): 283 WARNING @ Thu, 09 Dec 2021 03:03:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:03:11: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:03:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:03:19: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:03:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:03:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:03:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567192/SRX9567192.20_summits.bed INFO @ Thu, 09 Dec 2021 03:03:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (549 records, 4 fields): 1 millis CompletedMACS2peakCalling