Job ID = 14157851 SRX = SRX7879259 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30104381 spots for SRR11272874/SRR11272874.sra Written 30104381 spots for SRR11272874/SRR11272874.sra fastq に変換しました。 bowtie でマッピング中... Your job 14157988 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:26 30104381 reads; of these: 30104381 (100.00%) were unpaired; of these: 446560 (1.48%) aligned 0 times 24722082 (82.12%) aligned exactly 1 time 4935739 (16.40%) aligned >1 times 98.52% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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 16 files... [bam_rmdupse_core] 4396151 / 29657821 = 0.1482 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 @ Wed, 08 Dec 2021 11:39:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.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 @ Wed, 08 Dec 2021 11:39:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:39:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:39:59: 1000000 INFO @ Wed, 08 Dec 2021 11:40:06: 2000000 INFO @ Wed, 08 Dec 2021 11:40:13: 3000000 INFO @ Wed, 08 Dec 2021 11:40:20: 4000000 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 @ Wed, 08 Dec 2021 11:40:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.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 @ Wed, 08 Dec 2021 11:40:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:40:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:40:27: 5000000 INFO @ Wed, 08 Dec 2021 11:40:29: 1000000 INFO @ Wed, 08 Dec 2021 11:40:34: 6000000 INFO @ Wed, 08 Dec 2021 11:40:37: 2000000 INFO @ Wed, 08 Dec 2021 11:40:41: 7000000 INFO @ Wed, 08 Dec 2021 11:40:44: 3000000 INFO @ Wed, 08 Dec 2021 11:40:49: 8000000 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 @ Wed, 08 Dec 2021 11:40:52: 4000000 INFO @ Wed, 08 Dec 2021 11:40:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.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 @ Wed, 08 Dec 2021 11:40:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:40:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:40:56: 9000000 INFO @ Wed, 08 Dec 2021 11:40:59: 1000000 INFO @ Wed, 08 Dec 2021 11:40:59: 5000000 INFO @ Wed, 08 Dec 2021 11:41:04: 10000000 INFO @ Wed, 08 Dec 2021 11:41:05: 2000000 INFO @ Wed, 08 Dec 2021 11:41:07: 6000000 INFO @ Wed, 08 Dec 2021 11:41:11: 11000000 INFO @ Wed, 08 Dec 2021 11:41:12: 3000000 INFO @ Wed, 08 Dec 2021 11:41:14: 7000000 INFO @ Wed, 08 Dec 2021 11:41:19: 12000000 INFO @ Wed, 08 Dec 2021 11:41:19: 4000000 INFO @ Wed, 08 Dec 2021 11:41:22: 8000000 INFO @ Wed, 08 Dec 2021 11:41:26: 5000000 INFO @ Wed, 08 Dec 2021 11:41:27: 13000000 INFO @ Wed, 08 Dec 2021 11:41:29: 9000000 INFO @ Wed, 08 Dec 2021 11:41:33: 6000000 INFO @ Wed, 08 Dec 2021 11:41:34: 14000000 INFO @ Wed, 08 Dec 2021 11:41:37: 10000000 INFO @ Wed, 08 Dec 2021 11:41:40: 7000000 INFO @ Wed, 08 Dec 2021 11:41:42: 15000000 INFO @ Wed, 08 Dec 2021 11:41:45: 11000000 INFO @ Wed, 08 Dec 2021 11:41:46: 8000000 INFO @ Wed, 08 Dec 2021 11:41:49: 16000000 INFO @ Wed, 08 Dec 2021 11:41:52: 12000000 INFO @ Wed, 08 Dec 2021 11:41:53: 9000000 INFO @ Wed, 08 Dec 2021 11:41:57: 17000000 INFO @ Wed, 08 Dec 2021 11:42:00: 13000000 INFO @ Wed, 08 Dec 2021 11:42:00: 10000000 INFO @ Wed, 08 Dec 2021 11:42:05: 18000000 INFO @ Wed, 08 Dec 2021 11:42:07: 11000000 INFO @ Wed, 08 Dec 2021 11:42:08: 14000000 INFO @ Wed, 08 Dec 2021 11:42:12: 19000000 INFO @ Wed, 08 Dec 2021 11:42:14: 12000000 INFO @ Wed, 08 Dec 2021 11:42:15: 15000000 INFO @ Wed, 08 Dec 2021 11:42:20: 20000000 INFO @ Wed, 08 Dec 2021 11:42:21: 13000000 INFO @ Wed, 08 Dec 2021 11:42:23: 16000000 INFO @ Wed, 08 Dec 2021 11:42:27: 21000000 INFO @ Wed, 08 Dec 2021 11:42:27: 14000000 INFO @ Wed, 08 Dec 2021 11:42:30: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 11:42:34: 15000000 INFO @ Wed, 08 Dec 2021 11:42:35: 22000000 INFO @ Wed, 08 Dec 2021 11:42:38: 18000000 INFO @ Wed, 08 Dec 2021 11:42:41: 16000000 INFO @ Wed, 08 Dec 2021 11:42:42: 23000000 INFO @ Wed, 08 Dec 2021 11:42:46: 19000000 INFO @ Wed, 08 Dec 2021 11:42:48: 17000000 INFO @ Wed, 08 Dec 2021 11:42:50: 24000000 INFO @ Wed, 08 Dec 2021 11:42:53: 20000000 INFO @ Wed, 08 Dec 2021 11:42:55: 18000000 INFO @ Wed, 08 Dec 2021 11:42:57: 25000000 INFO @ Wed, 08 Dec 2021 11:42:59: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:42:59: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:42:59: #1 total tags in treatment: 25261670 INFO @ Wed, 08 Dec 2021 11:42:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:42:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 11:43:00: #1 tags after filtering in treatment: 25261670 INFO @ Wed, 08 Dec 2021 11:43:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:43:00: #1 finished! INFO @ Wed, 08 Dec 2021 11:43:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:43:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:43:01: 21000000 INFO @ Wed, 08 Dec 2021 11:43:01: #2 number of paired peaks: 146 WARNING @ Wed, 08 Dec 2021 11:43:01: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Wed, 08 Dec 2021 11:43:01: start model_add_line... INFO @ Wed, 08 Dec 2021 11:43:01: start X-correlation... INFO @ Wed, 08 Dec 2021 11:43:01: end of X-cor INFO @ Wed, 08 Dec 2021 11:43:01: #2 finished! INFO @ Wed, 08 Dec 2021 11:43:01: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 11:43:01: #2 alternative fragment length(s) may be 1,14,33,192,479,535,589,596 bps INFO @ Wed, 08 Dec 2021 11:43:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05_model.r WARNING @ Wed, 08 Dec 2021 11:43:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 11:43:01: #2 You may need to consider one of the other alternative d(s): 1,14,33,192,479,535,589,596 WARNING @ Wed, 08 Dec 2021 11:43:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 11:43:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:43:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:43:02: 19000000 INFO @ Wed, 08 Dec 2021 11:43:08: 20000000 INFO @ Wed, 08 Dec 2021 11:43:08: 22000000 INFO @ Wed, 08 Dec 2021 11:43:15: 21000000 INFO @ Wed, 08 Dec 2021 11:43:16: 23000000 INFO @ Wed, 08 Dec 2021 11:43:22: 22000000 INFO @ Wed, 08 Dec 2021 11:43:23: 24000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 11:43:28: 23000000 INFO @ Wed, 08 Dec 2021 11:43:31: 25000000 INFO @ Wed, 08 Dec 2021 11:43:33: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:43:33: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:43:33: #1 total tags in treatment: 25261670 INFO @ Wed, 08 Dec 2021 11:43:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:43:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 11:43:33: #1 tags after filtering in treatment: 25261670 INFO @ Wed, 08 Dec 2021 11:43:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:43:33: #1 finished! INFO @ Wed, 08 Dec 2021 11:43:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:43:35: #2 number of paired peaks: 146 WARNING @ Wed, 08 Dec 2021 11:43:35: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Wed, 08 Dec 2021 11:43:35: start model_add_line... INFO @ Wed, 08 Dec 2021 11:43:35: start X-correlation... INFO @ Wed, 08 Dec 2021 11:43:35: end of X-cor INFO @ Wed, 08 Dec 2021 11:43:35: #2 finished! INFO @ Wed, 08 Dec 2021 11:43:35: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 11:43:35: #2 alternative fragment length(s) may be 1,14,33,192,479,535,589,596 bps INFO @ Wed, 08 Dec 2021 11:43:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10_model.r WARNING @ Wed, 08 Dec 2021 11:43:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 11:43:35: #2 You may need to consider one of the other alternative d(s): 1,14,33,192,479,535,589,596 WARNING @ Wed, 08 Dec 2021 11:43:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 11:43:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:43:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:43:35: 24000000 INFO @ Wed, 08 Dec 2021 11:43:35: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:43:41: 25000000 INFO @ Wed, 08 Dec 2021 11:43:43: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:43:43: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:43:43: #1 total tags in treatment: 25261670 INFO @ Wed, 08 Dec 2021 11:43:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:43:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 11:43:43: #1 tags after filtering in treatment: 25261670 INFO @ Wed, 08 Dec 2021 11:43:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:43:43: #1 finished! INFO @ Wed, 08 Dec 2021 11:43:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:43:45: #2 number of paired peaks: 146 WARNING @ Wed, 08 Dec 2021 11:43:45: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Wed, 08 Dec 2021 11:43:45: start model_add_line... INFO @ Wed, 08 Dec 2021 11:43:45: start X-correlation... INFO @ Wed, 08 Dec 2021 11:43:45: end of X-cor INFO @ Wed, 08 Dec 2021 11:43:45: #2 finished! INFO @ Wed, 08 Dec 2021 11:43:45: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 11:43:45: #2 alternative fragment length(s) may be 1,14,33,192,479,535,589,596 bps INFO @ Wed, 08 Dec 2021 11:43:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20_model.r WARNING @ Wed, 08 Dec 2021 11:43:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 11:43:45: #2 You may need to consider one of the other alternative d(s): 1,14,33,192,479,535,589,596 WARNING @ Wed, 08 Dec 2021 11:43:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 11:43:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:43:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05_peaks.xls INFO @ Wed, 08 Dec 2021 11:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05_summits.bed INFO @ Wed, 08 Dec 2021 11:43:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 11:44:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:44:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:44:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10_peaks.xls INFO @ Wed, 08 Dec 2021 11:44:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:44:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10_summits.bed INFO @ Wed, 08 Dec 2021 11:44:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 11:44:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20_peaks.xls INFO @ Wed, 08 Dec 2021 11:44:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:44:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20_summits.bed INFO @ Wed, 08 Dec 2021 11:44:38: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling