Job ID = 16434968 SRX = SRX10435536 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16581305 spots for SRR14060936/SRR14060936.sra Written 16581305 spots for SRR14060936/SRR14060936.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435017 ("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: 00:05:17 16581305 reads; of these: 16581305 (100.00%) were unpaired; of these: 2190428 (13.21%) aligned 0 times 12045165 (72.64%) aligned exactly 1 time 2345712 (14.15%) aligned >1 times 86.79% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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] 2148315 / 14390877 = 0.1493 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 10:31:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.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 10:31:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:31:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:31:47: 1000000 INFO @ Tue, 02 Aug 2022 10:31:52: 2000000 INFO @ Tue, 02 Aug 2022 10:31:57: 3000000 INFO @ Tue, 02 Aug 2022 10:32:03: 4000000 INFO @ Tue, 02 Aug 2022 10:32:08: 5000000 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 10:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.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 10:32:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:32:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:32:14: 6000000 INFO @ Tue, 02 Aug 2022 10:32:17: 1000000 INFO @ Tue, 02 Aug 2022 10:32:20: 7000000 INFO @ Tue, 02 Aug 2022 10:32:23: 2000000 INFO @ Tue, 02 Aug 2022 10:32:25: 8000000 INFO @ Tue, 02 Aug 2022 10:32:29: 3000000 INFO @ Tue, 02 Aug 2022 10:32:31: 9000000 INFO @ Tue, 02 Aug 2022 10:32:35: 4000000 INFO @ Tue, 02 Aug 2022 10:32:37: 10000000 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 10:32:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.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 10:32:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:32:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:32:41: 5000000 INFO @ Tue, 02 Aug 2022 10:32:43: 11000000 INFO @ Tue, 02 Aug 2022 10:32:48: 6000000 INFO @ Tue, 02 Aug 2022 10:32:48: 1000000 INFO @ Tue, 02 Aug 2022 10:32:50: 12000000 INFO @ Tue, 02 Aug 2022 10:32:51: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:32:51: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:32:51: #1 total tags in treatment: 12242562 INFO @ Tue, 02 Aug 2022 10:32:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:32:51: #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 10:32:51: #1 tags after filtering in treatment: 12242562 INFO @ Tue, 02 Aug 2022 10:32:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:32:51: #1 finished! INFO @ Tue, 02 Aug 2022 10:32:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:32:52: #2 number of paired peaks: 459 WARNING @ Tue, 02 Aug 2022 10:32:52: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Tue, 02 Aug 2022 10:32:52: start model_add_line... INFO @ Tue, 02 Aug 2022 10:32:52: start X-correlation... INFO @ Tue, 02 Aug 2022 10:32:52: end of X-cor INFO @ Tue, 02 Aug 2022 10:32:52: #2 finished! INFO @ Tue, 02 Aug 2022 10:32:52: #2 predicted fragment length is 123 bps INFO @ Tue, 02 Aug 2022 10:32:52: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 02 Aug 2022 10:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.05_model.r WARNING @ Tue, 02 Aug 2022 10:32:52: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:32:52: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Tue, 02 Aug 2022 10:32:52: #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 10:32:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:32:54: 7000000 INFO @ Tue, 02 Aug 2022 10:32:54: 2000000 INFO @ Tue, 02 Aug 2022 10:33:00: 8000000 INFO @ Tue, 02 Aug 2022 10:33:00: 3000000 INFO @ Tue, 02 Aug 2022 10:33:06: 9000000 INFO @ Tue, 02 Aug 2022 10:33:07: 4000000 INFO @ Tue, 02 Aug 2022 10:33:12: 10000000 INFO @ Tue, 02 Aug 2022 10:33:13: 5000000 INFO @ Tue, 02 Aug 2022 10:33:18: 11000000 INFO @ Tue, 02 Aug 2022 10:33:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:33:19: 6000000 INFO @ Tue, 02 Aug 2022 10:33:24: 12000000 INFO @ Tue, 02 Aug 2022 10:33:25: 7000000 INFO @ Tue, 02 Aug 2022 10:33:25: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:33:25: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:33:25: #1 total tags in treatment: 12242562 INFO @ Tue, 02 Aug 2022 10:33:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:33:25: #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 10:33:25: #1 tags after filtering in treatment: 12242562 INFO @ Tue, 02 Aug 2022 10:33:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:33:25: #1 finished! INFO @ Tue, 02 Aug 2022 10:33:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:33:26: #2 number of paired peaks: 459 WARNING @ Tue, 02 Aug 2022 10:33:26: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Tue, 02 Aug 2022 10:33:26: start model_add_line... INFO @ Tue, 02 Aug 2022 10:33:26: start X-correlation... INFO @ Tue, 02 Aug 2022 10:33:26: end of X-cor INFO @ Tue, 02 Aug 2022 10:33:26: #2 finished! INFO @ Tue, 02 Aug 2022 10:33:26: #2 predicted fragment length is 123 bps INFO @ Tue, 02 Aug 2022 10:33:26: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 02 Aug 2022 10:33:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.10_model.r WARNING @ Tue, 02 Aug 2022 10:33:26: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:33:26: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Tue, 02 Aug 2022 10:33:26: #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 10:33:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:33:30: 8000000 INFO @ Tue, 02 Aug 2022 10:33:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:33:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:33:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.05_summits.bed INFO @ Tue, 02 Aug 2022 10:33:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1909 records, 4 fields): 91 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:33:36: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:33:41: 10000000 INFO @ Tue, 02 Aug 2022 10:33:46: 11000000 INFO @ Tue, 02 Aug 2022 10:33:52: 12000000 INFO @ Tue, 02 Aug 2022 10:33:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:33:53: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:33:53: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:33:53: #1 total tags in treatment: 12242562 INFO @ Tue, 02 Aug 2022 10:33:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:33:53: #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 10:33:53: #1 tags after filtering in treatment: 12242562 INFO @ Tue, 02 Aug 2022 10:33:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:33:53: #1 finished! INFO @ Tue, 02 Aug 2022 10:33:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:33:54: #2 number of paired peaks: 459 WARNING @ Tue, 02 Aug 2022 10:33:54: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Tue, 02 Aug 2022 10:33:54: start model_add_line... INFO @ Tue, 02 Aug 2022 10:33:54: start X-correlation... INFO @ Tue, 02 Aug 2022 10:33:54: end of X-cor INFO @ Tue, 02 Aug 2022 10:33:54: #2 finished! INFO @ Tue, 02 Aug 2022 10:33:54: #2 predicted fragment length is 123 bps INFO @ Tue, 02 Aug 2022 10:33:54: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 02 Aug 2022 10:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.20_model.r WARNING @ Tue, 02 Aug 2022 10:33:54: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:33:54: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Tue, 02 Aug 2022 10:33:54: #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 10:33:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:33:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.10_summits.bed INFO @ Tue, 02 Aug 2022 10:34:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1178 records, 4 fields): 90 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:34:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:34:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:34:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:34:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435536/SRX10435536.20_summits.bed INFO @ Tue, 02 Aug 2022 10:34:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (689 records, 4 fields): 7 millis CompletedMACS2peakCalling