Job ID = 16435595 SRX = SRX13110377 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:52:01 prefetch.2.10.7: 1) Downloading 'SRR16918047'... 2022-08-02T01:52:01 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:52:30 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:52:31 prefetch.2.10.7: 'SRR16918047' is valid 2022-08-02T01:52:31 prefetch.2.10.7: 1) 'SRR16918047' was downloaded successfully 2022-08-02T01:52:31 prefetch.2.10.7: 'SRR16918047' has 0 unresolved dependencies Read 17748326 spots for SRR16918047/SRR16918047.sra Written 17748326 spots for SRR16918047/SRR16918047.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436184 ("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: 00:05:47 17748326 reads; of these: 17748326 (100.00%) were unpaired; of these: 4082476 (23.00%) aligned 0 times 11610882 (65.42%) aligned exactly 1 time 2054968 (11.58%) aligned >1 times 77.00% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 1668098 / 13665850 = 0.1221 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 11:03:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.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 11:03:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:03:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:04:07: 1000000 INFO @ Tue, 02 Aug 2022 11:04:16: 2000000 INFO @ Tue, 02 Aug 2022 11:04:25: 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 11:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.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 11:04:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:04:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:04:33: 4000000 INFO @ Tue, 02 Aug 2022 11:04:36: 1000000 INFO @ Tue, 02 Aug 2022 11:04:42: 5000000 INFO @ Tue, 02 Aug 2022 11:04:45: 2000000 INFO @ Tue, 02 Aug 2022 11:04:51: 6000000 INFO @ Tue, 02 Aug 2022 11:04:54: 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 11:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.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 11:04:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:04:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:05:00: 7000000 INFO @ Tue, 02 Aug 2022 11:05:02: 4000000 INFO @ Tue, 02 Aug 2022 11:05:06: 1000000 INFO @ Tue, 02 Aug 2022 11:05:09: 8000000 INFO @ Tue, 02 Aug 2022 11:05:11: 5000000 INFO @ Tue, 02 Aug 2022 11:05:15: 2000000 INFO @ Tue, 02 Aug 2022 11:05:18: 9000000 INFO @ Tue, 02 Aug 2022 11:05:20: 6000000 INFO @ Tue, 02 Aug 2022 11:05:24: 3000000 INFO @ Tue, 02 Aug 2022 11:05:27: 10000000 INFO @ Tue, 02 Aug 2022 11:05:28: 7000000 INFO @ Tue, 02 Aug 2022 11:05:32: 4000000 INFO @ Tue, 02 Aug 2022 11:05:36: 11000000 INFO @ Tue, 02 Aug 2022 11:05:37: 8000000 INFO @ Tue, 02 Aug 2022 11:05:41: 5000000 INFO @ Tue, 02 Aug 2022 11:05:45: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:05:45: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:05:45: #1 total tags in treatment: 11997752 INFO @ Tue, 02 Aug 2022 11:05:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:05:45: #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 11:05:45: #1 tags after filtering in treatment: 11997752 INFO @ Tue, 02 Aug 2022 11:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:05:45: #1 finished! INFO @ Tue, 02 Aug 2022 11:05:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:05:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:05:46: #2 number of paired peaks: 241 WARNING @ Tue, 02 Aug 2022 11:05:46: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 02 Aug 2022 11:05:46: start model_add_line... INFO @ Tue, 02 Aug 2022 11:05:46: 9000000 INFO @ Tue, 02 Aug 2022 11:05:46: start X-correlation... INFO @ Tue, 02 Aug 2022 11:05:46: end of X-cor INFO @ Tue, 02 Aug 2022 11:05:46: #2 finished! INFO @ Tue, 02 Aug 2022 11:05:46: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 11:05:46: #2 alternative fragment length(s) may be 3,70,580 bps INFO @ Tue, 02 Aug 2022 11:05:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.05_model.r WARNING @ Tue, 02 Aug 2022 11:05:46: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:05:46: #2 You may need to consider one of the other alternative d(s): 3,70,580 WARNING @ Tue, 02 Aug 2022 11:05:46: #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 11:05:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:05:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:05:49: 6000000 INFO @ Tue, 02 Aug 2022 11:05:55: 10000000 INFO @ Tue, 02 Aug 2022 11:05:57: 7000000 INFO @ Tue, 02 Aug 2022 11:06:04: 11000000 INFO @ Tue, 02 Aug 2022 11:06:05: 8000000 INFO @ Tue, 02 Aug 2022 11:06:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:06:13: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:06:13: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:06:13: #1 total tags in treatment: 11997752 INFO @ Tue, 02 Aug 2022 11:06:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:06:13: #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 11:06:13: #1 tags after filtering in treatment: 11997752 INFO @ Tue, 02 Aug 2022 11:06:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:06:13: #1 finished! INFO @ Tue, 02 Aug 2022 11:06:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:06:14: 9000000 INFO @ Tue, 02 Aug 2022 11:06:14: #2 number of paired peaks: 241 WARNING @ Tue, 02 Aug 2022 11:06:14: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 02 Aug 2022 11:06:14: start model_add_line... INFO @ Tue, 02 Aug 2022 11:06:14: start X-correlation... INFO @ Tue, 02 Aug 2022 11:06:15: end of X-cor INFO @ Tue, 02 Aug 2022 11:06:15: #2 finished! INFO @ Tue, 02 Aug 2022 11:06:15: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 11:06:15: #2 alternative fragment length(s) may be 3,70,580 bps INFO @ Tue, 02 Aug 2022 11:06:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.10_model.r WARNING @ Tue, 02 Aug 2022 11:06:15: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:06:15: #2 You may need to consider one of the other alternative d(s): 3,70,580 WARNING @ Tue, 02 Aug 2022 11:06:15: #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 11:06:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:06:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:06:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:06:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:06:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.05_summits.bed INFO @ Tue, 02 Aug 2022 11:06:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:06:23: 10000000 INFO @ Tue, 02 Aug 2022 11:06:31: 11000000 INFO @ Tue, 02 Aug 2022 11:06:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:06:40: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:06:40: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:06:40: #1 total tags in treatment: 11997752 INFO @ Tue, 02 Aug 2022 11:06:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:06:40: #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 11:06:40: #1 tags after filtering in treatment: 11997752 INFO @ Tue, 02 Aug 2022 11:06:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:06:40: #1 finished! INFO @ Tue, 02 Aug 2022 11:06:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:06:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:06:41: #2 number of paired peaks: 241 WARNING @ Tue, 02 Aug 2022 11:06:41: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 02 Aug 2022 11:06:41: start model_add_line... INFO @ Tue, 02 Aug 2022 11:06:41: start X-correlation... INFO @ Tue, 02 Aug 2022 11:06:41: end of X-cor INFO @ Tue, 02 Aug 2022 11:06:41: #2 finished! INFO @ Tue, 02 Aug 2022 11:06:41: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 11:06:41: #2 alternative fragment length(s) may be 3,70,580 bps INFO @ Tue, 02 Aug 2022 11:06:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.20_model.r WARNING @ Tue, 02 Aug 2022 11:06:41: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:06:41: #2 You may need to consider one of the other alternative d(s): 3,70,580 WARNING @ Tue, 02 Aug 2022 11:06:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:06:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:06:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.10_summits.bed INFO @ Tue, 02 Aug 2022 11:06:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (382 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:07:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:07:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:07:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:07:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110377/SRX13110377.20_summits.bed INFO @ Tue, 02 Aug 2022 11:07:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 93 millis CompletedMACS2peakCalling BigWig に変換しました。