Job ID = 14159267 SRX = SRX3180812 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15659275 spots for SRR6030463/SRR6030463.sra Written 15659275 spots for SRR6030463/SRR6030463.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159481 ("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: 00:03:30 15659275 reads; of these: 15659275 (100.00%) were unpaired; of these: 955992 (6.10%) aligned 0 times 12193424 (77.87%) aligned exactly 1 time 2509859 (16.03%) aligned >1 times 93.90% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 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] 2754539 / 14703283 = 0.1873 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 20:41:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.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 20:41:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:41:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:41:42: 1000000 INFO @ Wed, 08 Dec 2021 20:41:48: 2000000 INFO @ Wed, 08 Dec 2021 20:41:54: 3000000 INFO @ Wed, 08 Dec 2021 20:42:01: 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 20:42:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.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 20:42:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:42:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:42:08: 5000000 INFO @ Wed, 08 Dec 2021 20:42:11: 1000000 INFO @ Wed, 08 Dec 2021 20:42:15: 6000000 INFO @ Wed, 08 Dec 2021 20:42:18: 2000000 INFO @ Wed, 08 Dec 2021 20:42:22: 7000000 INFO @ Wed, 08 Dec 2021 20:42:24: 3000000 INFO @ Wed, 08 Dec 2021 20:42:29: 8000000 INFO @ Wed, 08 Dec 2021 20:42:30: 4000000 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 20:42:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.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 20:42:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:42:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:42:36: 9000000 INFO @ Wed, 08 Dec 2021 20:42:37: 5000000 INFO @ Wed, 08 Dec 2021 20:42:42: 1000000 INFO @ Wed, 08 Dec 2021 20:42:43: 6000000 INFO @ Wed, 08 Dec 2021 20:42:44: 10000000 INFO @ Wed, 08 Dec 2021 20:42:49: 2000000 INFO @ Wed, 08 Dec 2021 20:42:49: 7000000 INFO @ Wed, 08 Dec 2021 20:42:51: 11000000 INFO @ Wed, 08 Dec 2021 20:42:56: 8000000 INFO @ Wed, 08 Dec 2021 20:42:56: 3000000 INFO @ Wed, 08 Dec 2021 20:42:58: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:42:58: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:42:58: #1 total tags in treatment: 11948744 INFO @ Wed, 08 Dec 2021 20:42:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:42:58: #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 20:42:58: #1 tags after filtering in treatment: 11948744 INFO @ Wed, 08 Dec 2021 20:42:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:42:58: #1 finished! INFO @ Wed, 08 Dec 2021 20:42:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:42:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:42:59: #2 number of paired peaks: 370 WARNING @ Wed, 08 Dec 2021 20:42:59: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Wed, 08 Dec 2021 20:42:59: start model_add_line... INFO @ Wed, 08 Dec 2021 20:42:59: start X-correlation... INFO @ Wed, 08 Dec 2021 20:42:59: end of X-cor INFO @ Wed, 08 Dec 2021 20:42:59: #2 finished! INFO @ Wed, 08 Dec 2021 20:42:59: #2 predicted fragment length is 46 bps INFO @ Wed, 08 Dec 2021 20:42:59: #2 alternative fragment length(s) may be 2,46,571 bps INFO @ Wed, 08 Dec 2021 20:42:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.05_model.r WARNING @ Wed, 08 Dec 2021 20:42:59: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:42:59: #2 You may need to consider one of the other alternative d(s): 2,46,571 WARNING @ Wed, 08 Dec 2021 20:42:59: #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 20:42:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:42:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:43:02: 9000000 INFO @ Wed, 08 Dec 2021 20:43:03: 4000000 INFO @ Wed, 08 Dec 2021 20:43:09: 10000000 INFO @ Wed, 08 Dec 2021 20:43:10: 5000000 INFO @ Wed, 08 Dec 2021 20:43:15: 11000000 INFO @ Wed, 08 Dec 2021 20:43:17: 6000000 INFO @ Wed, 08 Dec 2021 20:43:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:43:21: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:43:21: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:43:21: #1 total tags in treatment: 11948744 INFO @ Wed, 08 Dec 2021 20:43:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:43:21: #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 20:43:21: #1 tags after filtering in treatment: 11948744 INFO @ Wed, 08 Dec 2021 20:43:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:43:21: #1 finished! INFO @ Wed, 08 Dec 2021 20:43:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:43:22: #2 number of paired peaks: 370 WARNING @ Wed, 08 Dec 2021 20:43:22: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Wed, 08 Dec 2021 20:43:22: start model_add_line... INFO @ Wed, 08 Dec 2021 20:43:22: start X-correlation... INFO @ Wed, 08 Dec 2021 20:43:22: end of X-cor INFO @ Wed, 08 Dec 2021 20:43:22: #2 finished! INFO @ Wed, 08 Dec 2021 20:43:22: #2 predicted fragment length is 46 bps INFO @ Wed, 08 Dec 2021 20:43:22: #2 alternative fragment length(s) may be 2,46,571 bps INFO @ Wed, 08 Dec 2021 20:43:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.10_model.r WARNING @ Wed, 08 Dec 2021 20:43:22: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:43:22: #2 You may need to consider one of the other alternative d(s): 2,46,571 WARNING @ Wed, 08 Dec 2021 20:43:22: #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 20:43:22: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:43:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:43:24: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:43:31: 8000000 INFO @ Wed, 08 Dec 2021 20:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.05_summits.bed INFO @ Wed, 08 Dec 2021 20:43:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (698 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:43:37: 9000000 INFO @ Wed, 08 Dec 2021 20:43:44: 10000000 INFO @ Wed, 08 Dec 2021 20:43:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:43:51: 11000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:43:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:43:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:43:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.10_summits.bed INFO @ Wed, 08 Dec 2021 20:43:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (466 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:43:57: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:43:57: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:43:57: #1 total tags in treatment: 11948744 INFO @ Wed, 08 Dec 2021 20:43:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:43:57: #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 20:43:57: #1 tags after filtering in treatment: 11948744 INFO @ Wed, 08 Dec 2021 20:43:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:43:57: #1 finished! INFO @ Wed, 08 Dec 2021 20:43:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:43:58: #2 number of paired peaks: 370 WARNING @ Wed, 08 Dec 2021 20:43:58: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Wed, 08 Dec 2021 20:43:58: start model_add_line... INFO @ Wed, 08 Dec 2021 20:43:58: start X-correlation... INFO @ Wed, 08 Dec 2021 20:43:58: end of X-cor INFO @ Wed, 08 Dec 2021 20:43:58: #2 finished! INFO @ Wed, 08 Dec 2021 20:43:58: #2 predicted fragment length is 46 bps INFO @ Wed, 08 Dec 2021 20:43:58: #2 alternative fragment length(s) may be 2,46,571 bps INFO @ Wed, 08 Dec 2021 20:43:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.20_model.r WARNING @ Wed, 08 Dec 2021 20:43:58: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:43:58: #2 You may need to consider one of the other alternative d(s): 2,46,571 WARNING @ Wed, 08 Dec 2021 20:43:58: #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 20:43:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:44:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:44:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:44:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:44:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180812/SRX3180812.20_summits.bed INFO @ Wed, 08 Dec 2021 20:44:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 1 millis CompletedMACS2peakCalling