Job ID = 14160352 SRX = SRX9567176 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20331244 spots for SRR13125151/SRR13125151.sra Written 20331244 spots for SRR13125151/SRR13125151.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160604 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:02:29 20331244 reads; of these: 20331244 (100.00%) were paired; of these: 8086312 (39.77%) aligned concordantly 0 times 6904909 (33.96%) aligned concordantly exactly 1 time 5340023 (26.27%) aligned concordantly >1 times ---- 8086312 pairs aligned concordantly 0 times; of these: 4278153 (52.91%) aligned discordantly 1 time ---- 3808159 pairs aligned 0 times concordantly or discordantly; of these: 7616318 mates make up the pairs; of these: 5456096 (71.64%) aligned 0 times 917291 (12.04%) aligned exactly 1 time 1242931 (16.32%) aligned >1 times 86.58% overall alignment rate Time searching: 01:02:30 Overall time: 01:02:30 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 28 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] 13485689 / 16501152 = 0.8173 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 02:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.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 02:53:47: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:53:47: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:53:53: 1000000 INFO @ Thu, 09 Dec 2021 02:54:00: 2000000 INFO @ Thu, 09 Dec 2021 02:54:06: 3000000 INFO @ Thu, 09 Dec 2021 02:54:13: 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 02:54:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.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 02:54:17: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:54:17: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:54:20: 5000000 INFO @ Thu, 09 Dec 2021 02:54:26: 1000000 INFO @ Thu, 09 Dec 2021 02:54:28: 6000000 INFO @ Thu, 09 Dec 2021 02:54:35: 2000000 INFO @ Thu, 09 Dec 2021 02:54:36: 7000000 INFO @ Thu, 09 Dec 2021 02:54:44: 8000000 INFO @ Thu, 09 Dec 2021 02:54:44: 3000000 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 02:54:45: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:54:45: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:54:45: #1 total tags in treatment: 2299035 INFO @ Thu, 09 Dec 2021 02:54:45: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:54:45: #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 02:54:45: #1 tags after filtering in treatment: 1522321 INFO @ Thu, 09 Dec 2021 02:54:45: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 09 Dec 2021 02:54:45: #1 finished! INFO @ Thu, 09 Dec 2021 02:54:45: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:54:46: #2 number of paired peaks: 964 WARNING @ Thu, 09 Dec 2021 02:54:46: Fewer paired peaks (964) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 964 pairs to build model! INFO @ Thu, 09 Dec 2021 02:54:46: start model_add_line... INFO @ Thu, 09 Dec 2021 02:54:46: start X-correlation... INFO @ Thu, 09 Dec 2021 02:54:46: end of X-cor INFO @ Thu, 09 Dec 2021 02:54:46: #2 finished! INFO @ Thu, 09 Dec 2021 02:54:46: #2 predicted fragment length is 295 bps INFO @ Thu, 09 Dec 2021 02:54:46: #2 alternative fragment length(s) may be 295 bps INFO @ Thu, 09 Dec 2021 02:54:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.05_model.r WARNING @ Thu, 09 Dec 2021 02:54:46: #2 Since the d (295) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:54:46: #2 You may need to consider one of the other alternative d(s): 295 WARNING @ Thu, 09 Dec 2021 02:54:46: #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 02:54:46: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:54:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:54:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.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 02:54:47: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:54:47: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:54:51: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:54:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:54:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:54:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.05_summits.bed INFO @ Thu, 09 Dec 2021 02:54:52: Done! INFO @ Thu, 09 Dec 2021 02:54:52: 4000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (627 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:54:54: 1000000 INFO @ Thu, 09 Dec 2021 02:55:01: 5000000 INFO @ Thu, 09 Dec 2021 02:55:02: 2000000 INFO @ Thu, 09 Dec 2021 02:55:10: 3000000 INFO @ Thu, 09 Dec 2021 02:55:11: 6000000 INFO @ Thu, 09 Dec 2021 02:55:18: 4000000 INFO @ Thu, 09 Dec 2021 02:55:20: 7000000 INFO @ Thu, 09 Dec 2021 02:55:26: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:55:29: 8000000 INFO @ Thu, 09 Dec 2021 02:55:31: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:55:31: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:55:31: #1 total tags in treatment: 2299035 INFO @ Thu, 09 Dec 2021 02:55:31: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:55:31: #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 02:55:31: #1 tags after filtering in treatment: 1522321 INFO @ Thu, 09 Dec 2021 02:55:31: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 09 Dec 2021 02:55:31: #1 finished! INFO @ Thu, 09 Dec 2021 02:55:31: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:55:31: #2 number of paired peaks: 964 WARNING @ Thu, 09 Dec 2021 02:55:31: Fewer paired peaks (964) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 964 pairs to build model! INFO @ Thu, 09 Dec 2021 02:55:31: start model_add_line... INFO @ Thu, 09 Dec 2021 02:55:31: start X-correlation... INFO @ Thu, 09 Dec 2021 02:55:31: end of X-cor INFO @ Thu, 09 Dec 2021 02:55:31: #2 finished! INFO @ Thu, 09 Dec 2021 02:55:31: #2 predicted fragment length is 295 bps INFO @ Thu, 09 Dec 2021 02:55:31: #2 alternative fragment length(s) may be 295 bps INFO @ Thu, 09 Dec 2021 02:55:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.10_model.r WARNING @ Thu, 09 Dec 2021 02:55:31: #2 Since the d (295) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:55:31: #2 You may need to consider one of the other alternative d(s): 295 WARNING @ Thu, 09 Dec 2021 02:55:31: #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 02:55:31: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:55:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:55:34: 6000000 INFO @ Thu, 09 Dec 2021 02:55:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:55:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:55:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:55:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.10_summits.bed INFO @ Thu, 09 Dec 2021 02:55:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (486 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:55:40: 7000000 INFO @ Thu, 09 Dec 2021 02:55:47: 8000000 INFO @ Thu, 09 Dec 2021 02:55:48: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:55:48: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:55:48: #1 total tags in treatment: 2299035 INFO @ Thu, 09 Dec 2021 02:55:48: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:55:48: #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 02:55:48: #1 tags after filtering in treatment: 1522321 INFO @ Thu, 09 Dec 2021 02:55:48: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 09 Dec 2021 02:55:48: #1 finished! INFO @ Thu, 09 Dec 2021 02:55:48: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:55:49: #2 number of paired peaks: 964 WARNING @ Thu, 09 Dec 2021 02:55:49: Fewer paired peaks (964) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 964 pairs to build model! INFO @ Thu, 09 Dec 2021 02:55:49: start model_add_line... INFO @ Thu, 09 Dec 2021 02:55:49: start X-correlation... INFO @ Thu, 09 Dec 2021 02:55:49: end of X-cor INFO @ Thu, 09 Dec 2021 02:55:49: #2 finished! INFO @ Thu, 09 Dec 2021 02:55:49: #2 predicted fragment length is 295 bps INFO @ Thu, 09 Dec 2021 02:55:49: #2 alternative fragment length(s) may be 295 bps INFO @ Thu, 09 Dec 2021 02:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.20_model.r WARNING @ Thu, 09 Dec 2021 02:55:49: #2 Since the d (295) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:55:49: #2 You may need to consider one of the other alternative d(s): 295 WARNING @ Thu, 09 Dec 2021 02:55:49: #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 02:55:49: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:55:53: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:55:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:55:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:55:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567176/SRX9567176.20_summits.bed INFO @ Thu, 09 Dec 2021 02:55:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (383 records, 4 fields): 2 millis CompletedMACS2peakCalling