Job ID = 16434892 SRX = SRX10435516 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: 00:07:14 17538842 reads; of these: 17538842 (100.00%) were unpaired; of these: 712385 (4.06%) aligned 0 times 14234796 (81.16%) aligned exactly 1 time 2591661 (14.78%) aligned >1 times 95.94% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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] 1861471 / 16826457 = 0.1106 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:25:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.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, 02 Aug 2022 10:25:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:30: 1000000 INFO @ Tue, 02 Aug 2022 10:25:39: 2000000 INFO @ Tue, 02 Aug 2022 10:25:48: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:25:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.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, 02 Aug 2022 10:25:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:57: 4000000 INFO @ Tue, 02 Aug 2022 10:26:00: 1000000 INFO @ Tue, 02 Aug 2022 10:26:06: 5000000 INFO @ Tue, 02 Aug 2022 10:26:08: 2000000 INFO @ Tue, 02 Aug 2022 10:26:14: 6000000 INFO @ Tue, 02 Aug 2022 10:26:17: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.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, 02 Aug 2022 10:26:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:26:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:26:24: 7000000 INFO @ Tue, 02 Aug 2022 10:26:27: 4000000 INFO @ Tue, 02 Aug 2022 10:26:30: 1000000 INFO @ Tue, 02 Aug 2022 10:26:33: 8000000 INFO @ Tue, 02 Aug 2022 10:26:36: 5000000 INFO @ Tue, 02 Aug 2022 10:26:39: 2000000 INFO @ Tue, 02 Aug 2022 10:26:41: 9000000 INFO @ Tue, 02 Aug 2022 10:26:44: 6000000 INFO @ Tue, 02 Aug 2022 10:26:47: 3000000 INFO @ Tue, 02 Aug 2022 10:26:50: 10000000 INFO @ Tue, 02 Aug 2022 10:26:52: 7000000 INFO @ Tue, 02 Aug 2022 10:26:55: 4000000 INFO @ Tue, 02 Aug 2022 10:26:59: 11000000 INFO @ Tue, 02 Aug 2022 10:27:01: 8000000 INFO @ Tue, 02 Aug 2022 10:27:04: 5000000 INFO @ Tue, 02 Aug 2022 10:27:09: 9000000 INFO @ Tue, 02 Aug 2022 10:27:09: 12000000 INFO @ Tue, 02 Aug 2022 10:27:12: 6000000 INFO @ Tue, 02 Aug 2022 10:27:17: 10000000 INFO @ Tue, 02 Aug 2022 10:27:19: 13000000 INFO @ Tue, 02 Aug 2022 10:27:21: 7000000 INFO @ Tue, 02 Aug 2022 10:27:25: 11000000 INFO @ Tue, 02 Aug 2022 10:27:28: 14000000 INFO @ Tue, 02 Aug 2022 10:27:29: 8000000 INFO @ Tue, 02 Aug 2022 10:27:34: 12000000 INFO @ Tue, 02 Aug 2022 10:27:37: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:27:37: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:27:37: #1 total tags in treatment: 14964986 INFO @ Tue, 02 Aug 2022 10:27:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:27:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:27:37: #1 tags after filtering in treatment: 14964986 INFO @ Tue, 02 Aug 2022 10:27:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:27:37: #1 finished! INFO @ Tue, 02 Aug 2022 10:27:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:27:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:27:38: 9000000 INFO @ Tue, 02 Aug 2022 10:27:38: #2 number of paired peaks: 206 WARNING @ Tue, 02 Aug 2022 10:27:38: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 02 Aug 2022 10:27:38: start model_add_line... INFO @ Tue, 02 Aug 2022 10:27:39: start X-correlation... INFO @ Tue, 02 Aug 2022 10:27:39: end of X-cor INFO @ Tue, 02 Aug 2022 10:27:39: #2 finished! INFO @ Tue, 02 Aug 2022 10:27:39: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 10:27:39: #2 alternative fragment length(s) may be 3,75 bps INFO @ Tue, 02 Aug 2022 10:27:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.05_model.r WARNING @ Tue, 02 Aug 2022 10:27:39: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:27:39: #2 You may need to consider one of the other alternative d(s): 3,75 WARNING @ Tue, 02 Aug 2022 10:27:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:27:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:27:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:27:43: 13000000 INFO @ Tue, 02 Aug 2022 10:27:47: 10000000 INFO @ Tue, 02 Aug 2022 10:27:51: 14000000 INFO @ Tue, 02 Aug 2022 10:27:55: 11000000 INFO @ Tue, 02 Aug 2022 10:27:59: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:27:59: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:27:59: #1 total tags in treatment: 14964986 INFO @ Tue, 02 Aug 2022 10:27:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:27:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:27:59: #1 tags after filtering in treatment: 14964986 INFO @ Tue, 02 Aug 2022 10:27:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:27:59: #1 finished! INFO @ Tue, 02 Aug 2022 10:27:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:28:00: #2 number of paired peaks: 206 WARNING @ Tue, 02 Aug 2022 10:28:00: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 02 Aug 2022 10:28:00: start model_add_line... INFO @ Tue, 02 Aug 2022 10:28:00: start X-correlation... INFO @ Tue, 02 Aug 2022 10:28:00: end of X-cor INFO @ Tue, 02 Aug 2022 10:28:00: #2 finished! INFO @ Tue, 02 Aug 2022 10:28:00: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 10:28:00: #2 alternative fragment length(s) may be 3,75 bps INFO @ Tue, 02 Aug 2022 10:28:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.10_model.r WARNING @ Tue, 02 Aug 2022 10:28:00: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:28:00: #2 You may need to consider one of the other alternative d(s): 3,75 WARNING @ Tue, 02 Aug 2022 10:28:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:28:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:28:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:28:03: 12000000 INFO @ Tue, 02 Aug 2022 10:28:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:28:11: 13000000 INFO @ Tue, 02 Aug 2022 10:28:19: 14000000 INFO @ Tue, 02 Aug 2022 10:28:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:28:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:28:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.05_summits.bed INFO @ Tue, 02 Aug 2022 10:28:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (745 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:28:26: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:28:26: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:28:26: #1 total tags in treatment: 14964986 INFO @ Tue, 02 Aug 2022 10:28:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:28:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:28:26: #1 tags after filtering in treatment: 14964986 INFO @ Tue, 02 Aug 2022 10:28:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:28:26: #1 finished! INFO @ Tue, 02 Aug 2022 10:28:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:28:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:28:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:28:27: #2 number of paired peaks: 206 WARNING @ Tue, 02 Aug 2022 10:28:27: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 02 Aug 2022 10:28:27: start model_add_line... INFO @ Tue, 02 Aug 2022 10:28:27: start X-correlation... INFO @ Tue, 02 Aug 2022 10:28:27: end of X-cor INFO @ Tue, 02 Aug 2022 10:28:27: #2 finished! INFO @ Tue, 02 Aug 2022 10:28:27: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 10:28:27: #2 alternative fragment length(s) may be 3,75 bps INFO @ Tue, 02 Aug 2022 10:28:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.20_model.r WARNING @ Tue, 02 Aug 2022 10:28:27: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:28:27: #2 You may need to consider one of the other alternative d(s): 3,75 WARNING @ Tue, 02 Aug 2022 10:28:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:28:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:28:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:28:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:28:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:28:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.10_summits.bed INFO @ Tue, 02 Aug 2022 10:28:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (401 records, 4 fields): 32 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:28:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435516/SRX10435516.20_summits.bed INFO @ Tue, 02 Aug 2022 10:29:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。