Job ID = 14160831 SRX = SRX9567171 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: 00:00:00 Multiseed full-index search: 03:10:29 26549213 reads; of these: 26549213 (100.00%) were paired; of these: 6213034 (23.40%) aligned concordantly 0 times 5880939 (22.15%) aligned concordantly exactly 1 time 14455240 (54.45%) aligned concordantly >1 times ---- 6213034 pairs aligned concordantly 0 times; of these: 3001679 (48.31%) aligned discordantly 1 time ---- 3211355 pairs aligned 0 times concordantly or discordantly; of these: 6422710 mates make up the pairs; of these: 4154266 (64.68%) aligned 0 times 775688 (12.08%) aligned exactly 1 time 1492756 (23.24%) aligned >1 times 92.18% overall alignment rate Time searching: 03:10:29 Overall time: 03:10:29 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 36 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] 19038907 / 23279666 = 0.8178 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 07:56:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.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 07:56:29: #1 read tag files... INFO @ Thu, 09 Dec 2021 07:56:29: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 07:56:45: 1000000 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 07:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.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 07:56:59: #1 read tag files... INFO @ Thu, 09 Dec 2021 07:56:59: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 07:56:59: 2000000 INFO @ Thu, 09 Dec 2021 07:57:15: 1000000 INFO @ Thu, 09 Dec 2021 07:57:16: 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 07:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.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 07:57:29: #1 read tag files... INFO @ Thu, 09 Dec 2021 07:57:29: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 07:57:31: 4000000 INFO @ Thu, 09 Dec 2021 07:57:32: 2000000 INFO @ Thu, 09 Dec 2021 07:57:47: 1000000 INFO @ Thu, 09 Dec 2021 07:57:48: 5000000 INFO @ Thu, 09 Dec 2021 07:57:49: 3000000 INFO @ Thu, 09 Dec 2021 07:58:04: 6000000 INFO @ Thu, 09 Dec 2021 07:58:05: 4000000 INFO @ Thu, 09 Dec 2021 07:58:06: 2000000 INFO @ Thu, 09 Dec 2021 07:58:21: 7000000 INFO @ Thu, 09 Dec 2021 07:58:21: 5000000 INFO @ Thu, 09 Dec 2021 07:58:24: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 07:58:37: 6000000 INFO @ Thu, 09 Dec 2021 07:58:37: 8000000 INFO @ Thu, 09 Dec 2021 07:58:43: 4000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 07:58:53: 7000000 INFO @ Thu, 09 Dec 2021 07:58:53: 9000000 INFO @ Thu, 09 Dec 2021 07:59:01: 5000000 INFO @ Thu, 09 Dec 2021 07:59:08: 10000000 INFO @ Thu, 09 Dec 2021 07:59:10: 8000000 INFO @ Thu, 09 Dec 2021 07:59:20: 6000000 INFO @ Thu, 09 Dec 2021 07:59:23: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 07:59:23: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 07:59:23: #1 total tags in treatment: 3612719 INFO @ Thu, 09 Dec 2021 07:59:23: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 07:59:23: #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 07:59:23: #1 tags after filtering in treatment: 1618611 INFO @ Thu, 09 Dec 2021 07:59:23: #1 Redundant rate of treatment: 0.55 INFO @ Thu, 09 Dec 2021 07:59:23: #1 finished! INFO @ Thu, 09 Dec 2021 07:59:23: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 07:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 07:59:23: #2 number of paired peaks: 901 WARNING @ Thu, 09 Dec 2021 07:59:23: Fewer paired peaks (901) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 901 pairs to build model! INFO @ Thu, 09 Dec 2021 07:59:23: start model_add_line... INFO @ Thu, 09 Dec 2021 07:59:23: start X-correlation... INFO @ Thu, 09 Dec 2021 07:59:23: end of X-cor INFO @ Thu, 09 Dec 2021 07:59:23: #2 finished! INFO @ Thu, 09 Dec 2021 07:59:23: #2 predicted fragment length is 302 bps INFO @ Thu, 09 Dec 2021 07:59:23: #2 alternative fragment length(s) may be 302 bps INFO @ Thu, 09 Dec 2021 07:59:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.05_model.r WARNING @ Thu, 09 Dec 2021 07:59:23: #2 Since the d (302) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 07:59:23: #2 You may need to consider one of the other alternative d(s): 302 WARNING @ Thu, 09 Dec 2021 07:59:23: #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 07:59:23: #3 Call peaks... INFO @ Thu, 09 Dec 2021 07:59:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 07:59:27: 9000000 INFO @ Thu, 09 Dec 2021 07:59:31: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 07:59:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.05_peaks.xls INFO @ Thu, 09 Dec 2021 07:59:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 07:59:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.05_summits.bed INFO @ Thu, 09 Dec 2021 07:59:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 07:59:39: 7000000 INFO @ Thu, 09 Dec 2021 07:59:42: 10000000 INFO @ Thu, 09 Dec 2021 07:59:55: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 07:59:55: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 07:59:55: #1 total tags in treatment: 3612719 INFO @ Thu, 09 Dec 2021 07:59:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 07:59:55: #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 07:59:55: #1 tags after filtering in treatment: 1618611 INFO @ Thu, 09 Dec 2021 07:59:55: #1 Redundant rate of treatment: 0.55 INFO @ Thu, 09 Dec 2021 07:59:55: #1 finished! INFO @ Thu, 09 Dec 2021 07:59:55: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 07:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 07:59:55: #2 number of paired peaks: 901 WARNING @ Thu, 09 Dec 2021 07:59:55: Fewer paired peaks (901) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 901 pairs to build model! INFO @ Thu, 09 Dec 2021 07:59:55: start model_add_line... INFO @ Thu, 09 Dec 2021 07:59:55: start X-correlation... INFO @ Thu, 09 Dec 2021 07:59:55: end of X-cor INFO @ Thu, 09 Dec 2021 07:59:55: #2 finished! INFO @ Thu, 09 Dec 2021 07:59:55: #2 predicted fragment length is 302 bps INFO @ Thu, 09 Dec 2021 07:59:55: #2 alternative fragment length(s) may be 302 bps INFO @ Thu, 09 Dec 2021 07:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.10_model.r WARNING @ Thu, 09 Dec 2021 07:59:55: #2 Since the d (302) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 07:59:55: #2 You may need to consider one of the other alternative d(s): 302 WARNING @ Thu, 09 Dec 2021 07:59:55: #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 07:59:55: #3 Call peaks... INFO @ Thu, 09 Dec 2021 07:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 07:59:57: 8000000 INFO @ Thu, 09 Dec 2021 08:00:03: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 08:00:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.10_peaks.xls INFO @ Thu, 09 Dec 2021 08:00:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 08:00:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.10_summits.bed INFO @ Thu, 09 Dec 2021 08:00:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (566 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 08:00:14: 9000000 INFO @ Thu, 09 Dec 2021 08:00:32: 10000000 INFO @ Thu, 09 Dec 2021 08:00:46: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 08:00:46: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 08:00:46: #1 total tags in treatment: 3612719 INFO @ Thu, 09 Dec 2021 08:00:46: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 08:00:46: #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 08:00:46: #1 tags after filtering in treatment: 1618611 INFO @ Thu, 09 Dec 2021 08:00:46: #1 Redundant rate of treatment: 0.55 INFO @ Thu, 09 Dec 2021 08:00:46: #1 finished! INFO @ Thu, 09 Dec 2021 08:00:46: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 08:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 08:00:46: #2 number of paired peaks: 901 WARNING @ Thu, 09 Dec 2021 08:00:46: Fewer paired peaks (901) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 901 pairs to build model! INFO @ Thu, 09 Dec 2021 08:00:46: start model_add_line... INFO @ Thu, 09 Dec 2021 08:00:46: start X-correlation... INFO @ Thu, 09 Dec 2021 08:00:46: end of X-cor INFO @ Thu, 09 Dec 2021 08:00:46: #2 finished! INFO @ Thu, 09 Dec 2021 08:00:46: #2 predicted fragment length is 302 bps INFO @ Thu, 09 Dec 2021 08:00:46: #2 alternative fragment length(s) may be 302 bps INFO @ Thu, 09 Dec 2021 08:00:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.20_model.r WARNING @ Thu, 09 Dec 2021 08:00:46: #2 Since the d (302) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 08:00:46: #2 You may need to consider one of the other alternative d(s): 302 WARNING @ Thu, 09 Dec 2021 08:00:46: #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 08:00:46: #3 Call peaks... INFO @ Thu, 09 Dec 2021 08:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 08:00:53: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 08:00:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.20_peaks.xls INFO @ Thu, 09 Dec 2021 08:00:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 08:00:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567171/SRX9567171.20_summits.bed INFO @ Thu, 09 Dec 2021 08:00:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (452 records, 4 fields): 2 millis CompletedMACS2peakCalling