Job ID = 14160366 SRX = SRX9567183 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28062281 spots for SRR13125158/SRR13125158.sra Written 28062281 spots for SRR13125158/SRR13125158.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160652 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:12:35 28062281 reads; of these: 28062281 (100.00%) were paired; of these: 9555473 (34.05%) aligned concordantly 0 times 15951041 (56.84%) aligned concordantly exactly 1 time 2555767 (9.11%) aligned concordantly >1 times ---- 9555473 pairs aligned concordantly 0 times; of these: 5432571 (56.85%) aligned discordantly 1 time ---- 4122902 pairs aligned 0 times concordantly or discordantly; of these: 8245804 mates make up the pairs; of these: 5644704 (68.46%) aligned 0 times 1313773 (15.93%) aligned exactly 1 time 1287327 (15.61%) aligned >1 times 89.94% overall alignment rate Time searching: 01:12:36 Overall time: 01:12:36 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 40 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] 19257455 / 23914996 = 0.8052 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 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 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 03:18:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.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 03:18:48: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:18:48: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:18:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.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 03:18:48: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:18:48: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.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 03:18:49: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:18:49: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:19:00: 1000000 INFO @ Thu, 09 Dec 2021 03:19:00: 1000000 INFO @ Thu, 09 Dec 2021 03:19:00: 1000000 INFO @ Thu, 09 Dec 2021 03:19:10: 2000000 INFO @ Thu, 09 Dec 2021 03:19:11: 2000000 INFO @ Thu, 09 Dec 2021 03:19:12: 2000000 INFO @ Thu, 09 Dec 2021 03:19:20: 3000000 INFO @ Thu, 09 Dec 2021 03:19:21: 3000000 INFO @ Thu, 09 Dec 2021 03:19:22: 3000000 INFO @ Thu, 09 Dec 2021 03:19:30: 4000000 INFO @ Thu, 09 Dec 2021 03:19:31: 4000000 INFO @ Thu, 09 Dec 2021 03:19:32: 4000000 INFO @ Thu, 09 Dec 2021 03:19:41: 5000000 INFO @ Thu, 09 Dec 2021 03:19:42: 5000000 INFO @ Thu, 09 Dec 2021 03:19:43: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:19:52: 6000000 INFO @ Thu, 09 Dec 2021 03:19:53: 6000000 INFO @ Thu, 09 Dec 2021 03:19:55: 6000000 INFO @ Thu, 09 Dec 2021 03:20:04: 7000000 INFO @ Thu, 09 Dec 2021 03:20:04: 7000000 INFO @ Thu, 09 Dec 2021 03:20:06: 7000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:20:14: 8000000 INFO @ Thu, 09 Dec 2021 03:20:15: 8000000 INFO @ Thu, 09 Dec 2021 03:20:17: 8000000 INFO @ Thu, 09 Dec 2021 03:20:24: 9000000 INFO @ Thu, 09 Dec 2021 03:20:25: 9000000 INFO @ Thu, 09 Dec 2021 03:20:27: 9000000 INFO @ Thu, 09 Dec 2021 03:20:34: 10000000 INFO @ Thu, 09 Dec 2021 03:20:35: 10000000 INFO @ Thu, 09 Dec 2021 03:20:37: 10000000 INFO @ Thu, 09 Dec 2021 03:20:44: 11000000 INFO @ Thu, 09 Dec 2021 03:20:45: 11000000 INFO @ Thu, 09 Dec 2021 03:20:47: 11000000 INFO @ Thu, 09 Dec 2021 03:20:53: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:20:53: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:20:53: #1 total tags in treatment: 3646102 INFO @ Thu, 09 Dec 2021 03:20:53: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:20:53: #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 03:20:53: #1 tags after filtering in treatment: 3266897 INFO @ Thu, 09 Dec 2021 03:20:53: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:20:53: #1 finished! INFO @ Thu, 09 Dec 2021 03:20:53: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:20:54: #2 number of paired peaks: 758 WARNING @ Thu, 09 Dec 2021 03:20:54: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Thu, 09 Dec 2021 03:20:54: start model_add_line... INFO @ Thu, 09 Dec 2021 03:20:54: start X-correlation... INFO @ Thu, 09 Dec 2021 03:20:54: end of X-cor INFO @ Thu, 09 Dec 2021 03:20:54: #2 finished! INFO @ Thu, 09 Dec 2021 03:20:54: #2 predicted fragment length is 229 bps INFO @ Thu, 09 Dec 2021 03:20:54: #2 alternative fragment length(s) may be 229 bps INFO @ Thu, 09 Dec 2021 03:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.05_model.r WARNING @ Thu, 09 Dec 2021 03:20:54: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:20:54: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Thu, 09 Dec 2021 03:20:54: #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 03:20:54: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:20:54: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:20:54: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:20:54: #1 total tags in treatment: 3646102 INFO @ Thu, 09 Dec 2021 03:20:54: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:20:54: #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 03:20:54: #1 tags after filtering in treatment: 3266897 INFO @ Thu, 09 Dec 2021 03:20:54: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:20:54: #1 finished! INFO @ Thu, 09 Dec 2021 03:20:54: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:20:55: #2 number of paired peaks: 758 WARNING @ Thu, 09 Dec 2021 03:20:55: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Thu, 09 Dec 2021 03:20:55: start model_add_line... INFO @ Thu, 09 Dec 2021 03:20:55: start X-correlation... INFO @ Thu, 09 Dec 2021 03:20:55: end of X-cor INFO @ Thu, 09 Dec 2021 03:20:55: #2 finished! INFO @ Thu, 09 Dec 2021 03:20:55: #2 predicted fragment length is 229 bps INFO @ Thu, 09 Dec 2021 03:20:55: #2 alternative fragment length(s) may be 229 bps INFO @ Thu, 09 Dec 2021 03:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.10_model.r WARNING @ Thu, 09 Dec 2021 03:20:55: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:20:55: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Thu, 09 Dec 2021 03:20:55: #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 03:20:55: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:20:56: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:20:56: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:20:56: #1 total tags in treatment: 3646102 INFO @ Thu, 09 Dec 2021 03:20:56: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:20:56: #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 03:20:56: #1 tags after filtering in treatment: 3266897 INFO @ Thu, 09 Dec 2021 03:20:56: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:20:56: #1 finished! INFO @ Thu, 09 Dec 2021 03:20:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:20:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:20:57: #2 number of paired peaks: 758 WARNING @ Thu, 09 Dec 2021 03:20:57: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Thu, 09 Dec 2021 03:20:57: start model_add_line... INFO @ Thu, 09 Dec 2021 03:20:57: start X-correlation... INFO @ Thu, 09 Dec 2021 03:20:57: end of X-cor INFO @ Thu, 09 Dec 2021 03:20:57: #2 finished! INFO @ Thu, 09 Dec 2021 03:20:57: #2 predicted fragment length is 229 bps INFO @ Thu, 09 Dec 2021 03:20:57: #2 alternative fragment length(s) may be 229 bps INFO @ Thu, 09 Dec 2021 03:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.20_model.r WARNING @ Thu, 09 Dec 2021 03:20:57: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:20:57: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Thu, 09 Dec 2021 03:20:57: #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 03:20:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:20:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:21:02: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:21:04: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:21:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:21:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:21:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:21:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.05_summits.bed INFO @ Thu, 09 Dec 2021 03:21:06: Done! INFO @ Thu, 09 Dec 2021 03:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.10_summits.bed INFO @ Thu, 09 Dec 2021 03:21:07: Done! INFO @ Thu, 09 Dec 2021 03:21:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:21:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:21:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567183/SRX9567183.20_summits.bed INFO @ Thu, 09 Dec 2021 03:21:09: Done! pass1 - making usageList (7 chroms)pass1 - making usageList (7 chroms): 1 millis : 1 millis pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 2 millis pass2 - checking and writing primary data (525 records, 4 fields): 2 millis pass2 - checking and writing primary data (361 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling