Job ID = 14160619 SRX = SRX10399033 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12727087 spots for SRR14022421/SRR14022421.sra Written 12727087 spots for SRR14022421/SRR14022421.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160741 ("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: 00:03:27 12727087 reads; of these: 12727087 (100.00%) were unpaired; of these: 2425873 (19.06%) aligned 0 times 8556828 (67.23%) aligned exactly 1 time 1744386 (13.71%) aligned >1 times 80.94% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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 8 files... [bam_rmdupse_core] 972260 / 10301214 = 0.0944 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 03:32:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.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 03:32:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:32:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:32:43: 1000000 INFO @ Thu, 09 Dec 2021 03:32:48: 2000000 INFO @ Thu, 09 Dec 2021 03:32:54: 3000000 INFO @ Thu, 09 Dec 2021 03:32:59: 4000000 INFO @ Thu, 09 Dec 2021 03:33:04: 5000000 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 03:33:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.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 03:33:07: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:33:07: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:33:10: 6000000 INFO @ Thu, 09 Dec 2021 03:33:13: 1000000 INFO @ Thu, 09 Dec 2021 03:33:16: 7000000 INFO @ Thu, 09 Dec 2021 03:33:19: 2000000 INFO @ Thu, 09 Dec 2021 03:33:21: 8000000 INFO @ Thu, 09 Dec 2021 03:33:24: 3000000 INFO @ Thu, 09 Dec 2021 03:33:27: 9000000 INFO @ Thu, 09 Dec 2021 03:33:29: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:33:29: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:33:29: #1 total tags in treatment: 9328954 INFO @ Thu, 09 Dec 2021 03:33:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:33:29: #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 03:33:29: #1 tags after filtering in treatment: 9328954 INFO @ Thu, 09 Dec 2021 03:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:33:29: #1 finished! INFO @ Thu, 09 Dec 2021 03:33:29: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:33:29: #2 number of paired peaks: 377 WARNING @ Thu, 09 Dec 2021 03:33:29: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Thu, 09 Dec 2021 03:33:29: start model_add_line... INFO @ Thu, 09 Dec 2021 03:33:29: start X-correlation... INFO @ Thu, 09 Dec 2021 03:33:29: end of X-cor INFO @ Thu, 09 Dec 2021 03:33:29: #2 finished! INFO @ Thu, 09 Dec 2021 03:33:29: #2 predicted fragment length is 87 bps INFO @ Thu, 09 Dec 2021 03:33:29: #2 alternative fragment length(s) may be 87 bps INFO @ Thu, 09 Dec 2021 03:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.05_model.r WARNING @ Thu, 09 Dec 2021 03:33:29: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:33:29: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Thu, 09 Dec 2021 03:33:29: #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 03:33:29: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:33:30: 4000000 INFO @ Thu, 09 Dec 2021 03:33:35: 5000000 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 03:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.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 03:33:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:33:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:33:41: 6000000 INFO @ Thu, 09 Dec 2021 03:33:44: 1000000 INFO @ Thu, 09 Dec 2021 03:33:47: 7000000 INFO @ Thu, 09 Dec 2021 03:33:48: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:33:51: 2000000 INFO @ Thu, 09 Dec 2021 03:33:53: 8000000 INFO @ Thu, 09 Dec 2021 03:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.05_summits.bed INFO @ Thu, 09 Dec 2021 03:33:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1132 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:33:58: 3000000 INFO @ Thu, 09 Dec 2021 03:33:59: 9000000 INFO @ Thu, 09 Dec 2021 03:34:01: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:34:01: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:34:01: #1 total tags in treatment: 9328954 INFO @ Thu, 09 Dec 2021 03:34:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:34:01: #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 03:34:01: #1 tags after filtering in treatment: 9328954 INFO @ Thu, 09 Dec 2021 03:34:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:34:01: #1 finished! INFO @ Thu, 09 Dec 2021 03:34:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:34:01: #2 number of paired peaks: 377 WARNING @ Thu, 09 Dec 2021 03:34:01: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Thu, 09 Dec 2021 03:34:01: start model_add_line... INFO @ Thu, 09 Dec 2021 03:34:01: start X-correlation... INFO @ Thu, 09 Dec 2021 03:34:01: end of X-cor INFO @ Thu, 09 Dec 2021 03:34:01: #2 finished! INFO @ Thu, 09 Dec 2021 03:34:01: #2 predicted fragment length is 87 bps INFO @ Thu, 09 Dec 2021 03:34:01: #2 alternative fragment length(s) may be 87 bps INFO @ Thu, 09 Dec 2021 03:34:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.10_model.r WARNING @ Thu, 09 Dec 2021 03:34:01: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:34:01: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Thu, 09 Dec 2021 03:34:01: #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 03:34:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:34:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:34:04: 4000000 INFO @ Thu, 09 Dec 2021 03:34:11: 5000000 INFO @ Thu, 09 Dec 2021 03:34:18: 6000000 INFO @ Thu, 09 Dec 2021 03:34:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:34:24: 7000000 INFO @ Thu, 09 Dec 2021 03:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.10_summits.bed INFO @ Thu, 09 Dec 2021 03:34:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (691 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:34:31: 8000000 INFO @ Thu, 09 Dec 2021 03:34:37: 9000000 INFO @ Thu, 09 Dec 2021 03:34:39: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:34:39: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:34:39: #1 total tags in treatment: 9328954 INFO @ Thu, 09 Dec 2021 03:34:39: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:34:39: #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 03:34:39: #1 tags after filtering in treatment: 9328954 INFO @ Thu, 09 Dec 2021 03:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:34:39: #1 finished! INFO @ Thu, 09 Dec 2021 03:34:39: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:34:40: #2 number of paired peaks: 377 WARNING @ Thu, 09 Dec 2021 03:34:40: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Thu, 09 Dec 2021 03:34:40: start model_add_line... INFO @ Thu, 09 Dec 2021 03:34:40: start X-correlation... INFO @ Thu, 09 Dec 2021 03:34:40: end of X-cor INFO @ Thu, 09 Dec 2021 03:34:40: #2 finished! INFO @ Thu, 09 Dec 2021 03:34:40: #2 predicted fragment length is 87 bps INFO @ Thu, 09 Dec 2021 03:34:40: #2 alternative fragment length(s) may be 87 bps INFO @ Thu, 09 Dec 2021 03:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.20_model.r WARNING @ Thu, 09 Dec 2021 03:34:40: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:34:40: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Thu, 09 Dec 2021 03:34:40: #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 03:34:40: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:34:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:34:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:35:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:35:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:35:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399033/SRX10399033.20_summits.bed INFO @ Thu, 09 Dec 2021 03:35:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (312 records, 4 fields): 1 millis CompletedMACS2peakCalling