Job ID = 6626609 SRX = SRX7630548 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE 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: 00:07:08 37026751 reads; of these: 37026751 (100.00%) were unpaired; of these: 11645874 (31.45%) aligned 0 times 21223692 (57.32%) aligned exactly 1 time 4157185 (11.23%) aligned >1 times 68.55% overall alignment rate Time searching: 00:07:08 Overall time: 00:07:08 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 12 files... [bam_rmdupse_core] 7566947 / 25380877 = 0.2981 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.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 @ Tue, 14 Jul 2020 08:03:04: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:03:04: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:03:09: 1000000 INFO @ Tue, 14 Jul 2020 08:03:15: 2000000 INFO @ Tue, 14 Jul 2020 08:03:20: 3000000 INFO @ Tue, 14 Jul 2020 08:03:25: 4000000 INFO @ Tue, 14 Jul 2020 08:03:30: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:03:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.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 @ Tue, 14 Jul 2020 08:03:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:03:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:03:36: 6000000 INFO @ Tue, 14 Jul 2020 08:03:39: 1000000 INFO @ Tue, 14 Jul 2020 08:03:41: 7000000 INFO @ Tue, 14 Jul 2020 08:03:44: 2000000 INFO @ Tue, 14 Jul 2020 08:03:46: 8000000 INFO @ Tue, 14 Jul 2020 08:03:49: 3000000 INFO @ Tue, 14 Jul 2020 08:03:51: 9000000 INFO @ Tue, 14 Jul 2020 08:03:55: 4000000 INFO @ Tue, 14 Jul 2020 08:03:57: 10000000 INFO @ Tue, 14 Jul 2020 08:04:00: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:04:02: 11000000 INFO @ Tue, 14 Jul 2020 08:04:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.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 @ Tue, 14 Jul 2020 08:04:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:04:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:04:05: 6000000 INFO @ Tue, 14 Jul 2020 08:04:07: 12000000 INFO @ Tue, 14 Jul 2020 08:04:09: 1000000 INFO @ Tue, 14 Jul 2020 08:04:11: 7000000 INFO @ Tue, 14 Jul 2020 08:04:13: 13000000 INFO @ Tue, 14 Jul 2020 08:04:14: 2000000 INFO @ Tue, 14 Jul 2020 08:04:16: 8000000 INFO @ Tue, 14 Jul 2020 08:04:18: 14000000 INFO @ Tue, 14 Jul 2020 08:04:20: 3000000 INFO @ Tue, 14 Jul 2020 08:04:21: 9000000 INFO @ Tue, 14 Jul 2020 08:04:24: 15000000 INFO @ Tue, 14 Jul 2020 08:04:25: 4000000 INFO @ Tue, 14 Jul 2020 08:04:27: 10000000 INFO @ Tue, 14 Jul 2020 08:04:29: 16000000 INFO @ Tue, 14 Jul 2020 08:04:30: 5000000 INFO @ Tue, 14 Jul 2020 08:04:32: 11000000 INFO @ Tue, 14 Jul 2020 08:04:35: 17000000 INFO @ Tue, 14 Jul 2020 08:04:36: 6000000 INFO @ Tue, 14 Jul 2020 08:04:37: 12000000 INFO @ Tue, 14 Jul 2020 08:04:39: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:04:39: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:04:39: #1 total tags in treatment: 17813930 INFO @ Tue, 14 Jul 2020 08:04:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:04:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:04:39: #1 tags after filtering in treatment: 17813930 INFO @ Tue, 14 Jul 2020 08:04:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:04:39: #1 finished! INFO @ Tue, 14 Jul 2020 08:04:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:04:41: #2 number of paired peaks: 315 WARNING @ Tue, 14 Jul 2020 08:04:41: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 14 Jul 2020 08:04:41: start model_add_line... INFO @ Tue, 14 Jul 2020 08:04:41: start X-correlation... INFO @ Tue, 14 Jul 2020 08:04:41: end of X-cor INFO @ Tue, 14 Jul 2020 08:04:41: #2 finished! INFO @ Tue, 14 Jul 2020 08:04:41: #2 predicted fragment length is 71 bps INFO @ Tue, 14 Jul 2020 08:04:41: #2 alternative fragment length(s) may be 3,68,71,596 bps INFO @ Tue, 14 Jul 2020 08:04:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.05_model.r WARNING @ Tue, 14 Jul 2020 08:04:41: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:04:41: #2 You may need to consider one of the other alternative d(s): 3,68,71,596 WARNING @ Tue, 14 Jul 2020 08:04:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:04:41: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:04:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:04:41: 7000000 INFO @ Tue, 14 Jul 2020 08:04:43: 13000000 INFO @ Tue, 14 Jul 2020 08:04:47: 8000000 INFO @ Tue, 14 Jul 2020 08:04:48: 14000000 INFO @ Tue, 14 Jul 2020 08:04:52: 9000000 INFO @ Tue, 14 Jul 2020 08:04:53: 15000000 INFO @ Tue, 14 Jul 2020 08:04:57: 10000000 INFO @ Tue, 14 Jul 2020 08:04:58: 16000000 INFO @ Tue, 14 Jul 2020 08:05:02: 11000000 INFO @ Tue, 14 Jul 2020 08:05:04: 17000000 INFO @ Tue, 14 Jul 2020 08:05:08: 12000000 INFO @ Tue, 14 Jul 2020 08:05:08: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:05:08: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:05:08: #1 total tags in treatment: 17813930 INFO @ Tue, 14 Jul 2020 08:05:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:05:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:05:09: #1 tags after filtering in treatment: 17813930 INFO @ Tue, 14 Jul 2020 08:05:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:05:09: #1 finished! INFO @ Tue, 14 Jul 2020 08:05:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:05:10: #2 number of paired peaks: 315 WARNING @ Tue, 14 Jul 2020 08:05:10: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 14 Jul 2020 08:05:10: start model_add_line... INFO @ Tue, 14 Jul 2020 08:05:10: start X-correlation... INFO @ Tue, 14 Jul 2020 08:05:10: end of X-cor INFO @ Tue, 14 Jul 2020 08:05:10: #2 finished! INFO @ Tue, 14 Jul 2020 08:05:10: #2 predicted fragment length is 71 bps INFO @ Tue, 14 Jul 2020 08:05:10: #2 alternative fragment length(s) may be 3,68,71,596 bps INFO @ Tue, 14 Jul 2020 08:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.10_model.r WARNING @ Tue, 14 Jul 2020 08:05:10: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:05:10: #2 You may need to consider one of the other alternative d(s): 3,68,71,596 WARNING @ Tue, 14 Jul 2020 08:05:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:05:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:05:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:05:13: 13000000 INFO @ Tue, 14 Jul 2020 08:05:18: 14000000 INFO @ Tue, 14 Jul 2020 08:05:23: 15000000 INFO @ Tue, 14 Jul 2020 08:05:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:05:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:05:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.05_summits.bed INFO @ Tue, 14 Jul 2020 08:05:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1807 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:05:28: 16000000 INFO @ Tue, 14 Jul 2020 08:05:34: 17000000 INFO @ Tue, 14 Jul 2020 08:05:38: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:05:38: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:05:38: #1 total tags in treatment: 17813930 INFO @ Tue, 14 Jul 2020 08:05:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:05:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:05:38: #1 tags after filtering in treatment: 17813930 INFO @ Tue, 14 Jul 2020 08:05:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:05:38: #1 finished! INFO @ Tue, 14 Jul 2020 08:05:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:05:39: #2 number of paired peaks: 315 WARNING @ Tue, 14 Jul 2020 08:05:39: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 14 Jul 2020 08:05:39: start model_add_line... INFO @ Tue, 14 Jul 2020 08:05:40: start X-correlation... INFO @ Tue, 14 Jul 2020 08:05:40: end of X-cor INFO @ Tue, 14 Jul 2020 08:05:40: #2 finished! INFO @ Tue, 14 Jul 2020 08:05:40: #2 predicted fragment length is 71 bps INFO @ Tue, 14 Jul 2020 08:05:40: #2 alternative fragment length(s) may be 3,68,71,596 bps INFO @ Tue, 14 Jul 2020 08:05:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.20_model.r WARNING @ Tue, 14 Jul 2020 08:05:40: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:05:40: #2 You may need to consider one of the other alternative d(s): 3,68,71,596 WARNING @ Tue, 14 Jul 2020 08:05:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:05:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:05:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:05:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:05:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:05:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:05:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.10_summits.bed INFO @ Tue, 14 Jul 2020 08:05:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (873 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:06:11: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:06:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:06:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:06:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630548/SRX7630548.20_summits.bed INFO @ Tue, 14 Jul 2020 08:06:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (388 records, 4 fields): 2 millis CompletedMACS2peakCalling