Job ID = 14157867 SRX = SRX6799185 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34054065 spots for SRR10065392/SRR10065392.sra Written 34054065 spots for SRR10065392/SRR10065392.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158036 ("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: 00:07:36 34054065 reads; of these: 34054065 (100.00%) were unpaired; of these: 2235614 (6.56%) aligned 0 times 24303183 (71.37%) aligned exactly 1 time 7515268 (22.07%) aligned >1 times 93.44% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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] 8936797 / 31818451 = 0.2809 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 12:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.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 12:04:27: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:04:27: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:04:33: 1000000 INFO @ Wed, 08 Dec 2021 12:04:38: 2000000 INFO @ Wed, 08 Dec 2021 12:04:43: 3000000 INFO @ Wed, 08 Dec 2021 12:04:49: 4000000 INFO @ Wed, 08 Dec 2021 12:04:54: 5000000 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 12:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.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 12:04:57: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:04:57: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:05:00: 6000000 INFO @ Wed, 08 Dec 2021 12:05:02: 1000000 INFO @ Wed, 08 Dec 2021 12:05:05: 7000000 INFO @ Wed, 08 Dec 2021 12:05:07: 2000000 INFO @ Wed, 08 Dec 2021 12:05:11: 8000000 INFO @ Wed, 08 Dec 2021 12:05:12: 3000000 INFO @ Wed, 08 Dec 2021 12:05:17: 9000000 INFO @ Wed, 08 Dec 2021 12:05:17: 4000000 INFO @ Wed, 08 Dec 2021 12:05:22: 10000000 INFO @ Wed, 08 Dec 2021 12:05:23: 5000000 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 12:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.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 12:05:27: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:05:27: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:05:28: 6000000 INFO @ Wed, 08 Dec 2021 12:05:28: 11000000 INFO @ Wed, 08 Dec 2021 12:05:32: 1000000 INFO @ Wed, 08 Dec 2021 12:05:33: 7000000 INFO @ Wed, 08 Dec 2021 12:05:34: 12000000 INFO @ Wed, 08 Dec 2021 12:05:38: 2000000 INFO @ Wed, 08 Dec 2021 12:05:39: 8000000 INFO @ Wed, 08 Dec 2021 12:05:40: 13000000 INFO @ Wed, 08 Dec 2021 12:05:43: 3000000 INFO @ Wed, 08 Dec 2021 12:05:44: 9000000 INFO @ Wed, 08 Dec 2021 12:05:46: 14000000 INFO @ Wed, 08 Dec 2021 12:05:48: 4000000 INFO @ Wed, 08 Dec 2021 12:05:49: 10000000 INFO @ Wed, 08 Dec 2021 12:05:52: 15000000 INFO @ Wed, 08 Dec 2021 12:05:54: 5000000 INFO @ Wed, 08 Dec 2021 12:05:55: 11000000 INFO @ Wed, 08 Dec 2021 12:05:58: 16000000 INFO @ Wed, 08 Dec 2021 12:05:59: 6000000 INFO @ Wed, 08 Dec 2021 12:06:00: 12000000 INFO @ Wed, 08 Dec 2021 12:06:03: 17000000 INFO @ Wed, 08 Dec 2021 12:06:04: 7000000 INFO @ Wed, 08 Dec 2021 12:06:06: 13000000 INFO @ Wed, 08 Dec 2021 12:06:09: 18000000 INFO @ Wed, 08 Dec 2021 12:06:09: 8000000 INFO @ Wed, 08 Dec 2021 12:06:11: 14000000 INFO @ Wed, 08 Dec 2021 12:06:15: 9000000 INFO @ Wed, 08 Dec 2021 12:06:15: 19000000 INFO @ Wed, 08 Dec 2021 12:06:16: 15000000 INFO @ Wed, 08 Dec 2021 12:06:20: 10000000 INFO @ Wed, 08 Dec 2021 12:06:21: 20000000 INFO @ Wed, 08 Dec 2021 12:06:22: 16000000 INFO @ Wed, 08 Dec 2021 12:06:25: 11000000 INFO @ Wed, 08 Dec 2021 12:06:27: 21000000 INFO @ Wed, 08 Dec 2021 12:06:27: 17000000 INFO @ Wed, 08 Dec 2021 12:06:30: 12000000 INFO @ Wed, 08 Dec 2021 12:06:33: 18000000 INFO @ Wed, 08 Dec 2021 12:06:33: 22000000 INFO @ Wed, 08 Dec 2021 12:06:36: 13000000 INFO @ Wed, 08 Dec 2021 12:06:38: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:06:38: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:06:38: #1 total tags in treatment: 22881654 INFO @ Wed, 08 Dec 2021 12:06:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:06:38: #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 12:06:38: 19000000 INFO @ Wed, 08 Dec 2021 12:06:38: #1 tags after filtering in treatment: 22881654 INFO @ Wed, 08 Dec 2021 12:06:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:06:38: #1 finished! INFO @ Wed, 08 Dec 2021 12:06:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:06:40: #2 number of paired peaks: 219 WARNING @ Wed, 08 Dec 2021 12:06:40: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Wed, 08 Dec 2021 12:06:40: start model_add_line... INFO @ Wed, 08 Dec 2021 12:06:40: start X-correlation... INFO @ Wed, 08 Dec 2021 12:06:40: end of X-cor INFO @ Wed, 08 Dec 2021 12:06:40: #2 finished! INFO @ Wed, 08 Dec 2021 12:06:40: #2 predicted fragment length is 59 bps INFO @ Wed, 08 Dec 2021 12:06:40: #2 alternative fragment length(s) may be 2,49,59,85 bps INFO @ Wed, 08 Dec 2021 12:06:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05_model.r WARNING @ Wed, 08 Dec 2021 12:06:40: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:06:40: #2 You may need to consider one of the other alternative d(s): 2,49,59,85 WARNING @ Wed, 08 Dec 2021 12:06:40: #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 12:06:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:06:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:06:41: 14000000 INFO @ Wed, 08 Dec 2021 12:06:43: 20000000 INFO @ Wed, 08 Dec 2021 12:06:46: 15000000 INFO @ Wed, 08 Dec 2021 12:06:49: 21000000 INFO @ Wed, 08 Dec 2021 12:06:51: 16000000 INFO @ Wed, 08 Dec 2021 12:06:54: 22000000 INFO @ Wed, 08 Dec 2021 12:06:57: 17000000 INFO @ Wed, 08 Dec 2021 12:06:59: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:06:59: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:06:59: #1 total tags in treatment: 22881654 INFO @ Wed, 08 Dec 2021 12:06:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:06:59: #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 12:06:59: #1 tags after filtering in treatment: 22881654 INFO @ Wed, 08 Dec 2021 12:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:06:59: #1 finished! INFO @ Wed, 08 Dec 2021 12:06:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:07:01: #2 number of paired peaks: 219 WARNING @ Wed, 08 Dec 2021 12:07:01: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Wed, 08 Dec 2021 12:07:01: start model_add_line... INFO @ Wed, 08 Dec 2021 12:07:01: start X-correlation... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:07:01: end of X-cor INFO @ Wed, 08 Dec 2021 12:07:01: #2 finished! INFO @ Wed, 08 Dec 2021 12:07:01: #2 predicted fragment length is 59 bps INFO @ Wed, 08 Dec 2021 12:07:01: #2 alternative fragment length(s) may be 2,49,59,85 bps INFO @ Wed, 08 Dec 2021 12:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10_model.r WARNING @ Wed, 08 Dec 2021 12:07:01: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:07:01: #2 You may need to consider one of the other alternative d(s): 2,49,59,85 WARNING @ Wed, 08 Dec 2021 12:07:01: #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 12:07:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:07:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:07:02: 18000000 INFO @ Wed, 08 Dec 2021 12:07:07: 19000000 INFO @ Wed, 08 Dec 2021 12:07:11: 20000000 INFO @ Wed, 08 Dec 2021 12:07:16: 21000000 INFO @ Wed, 08 Dec 2021 12:07:18: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:07:21: 22000000 INFO @ Wed, 08 Dec 2021 12:07:26: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:07:26: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:07:26: #1 total tags in treatment: 22881654 INFO @ Wed, 08 Dec 2021 12:07:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:07:26: #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 12:07:26: #1 tags after filtering in treatment: 22881654 INFO @ Wed, 08 Dec 2021 12:07:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:07:26: #1 finished! INFO @ Wed, 08 Dec 2021 12:07:26: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:07:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:07:27: #2 number of paired peaks: 219 WARNING @ Wed, 08 Dec 2021 12:07:27: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Wed, 08 Dec 2021 12:07:27: start model_add_line... INFO @ Wed, 08 Dec 2021 12:07:27: start X-correlation... INFO @ Wed, 08 Dec 2021 12:07:28: end of X-cor INFO @ Wed, 08 Dec 2021 12:07:28: #2 finished! INFO @ Wed, 08 Dec 2021 12:07:28: #2 predicted fragment length is 59 bps INFO @ Wed, 08 Dec 2021 12:07:28: #2 alternative fragment length(s) may be 2,49,59,85 bps INFO @ Wed, 08 Dec 2021 12:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20_model.r WARNING @ Wed, 08 Dec 2021 12:07:28: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:07:28: #2 You may need to consider one of the other alternative d(s): 2,49,59,85 WARNING @ Wed, 08 Dec 2021 12:07:28: #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 12:07:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:07:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:07:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:07:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05_summits.bed INFO @ Wed, 08 Dec 2021 12:07:38: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9793 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:07:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:08:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:08:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:08:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10_summits.bed INFO @ Wed, 08 Dec 2021 12:08:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3248 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:08:05: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:08:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:08:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:08:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20_summits.bed INFO @ Wed, 08 Dec 2021 12:08:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (485 records, 4 fields): 2 millis CompletedMACS2peakCalling