Job ID = 14159233 SRX = SRX3180802 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18304315 spots for SRR6030453/SRR6030453.sra Written 18304315 spots for SRR6030453/SRR6030453.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159444 ("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: 00:05:10 18304315 reads; of these: 18304315 (100.00%) were unpaired; of these: 1590176 (8.69%) aligned 0 times 13338012 (72.87%) aligned exactly 1 time 3376127 (18.44%) aligned >1 times 91.31% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 4815620 / 16714139 = 0.2881 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 20:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.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 20:34:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:34:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:34:38: 1000000 INFO @ Wed, 08 Dec 2021 20:34:48: 2000000 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 20:34:57: 3000000 INFO @ Wed, 08 Dec 2021 20:34:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.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 20:34:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:34:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:35:06: 4000000 INFO @ Wed, 08 Dec 2021 20:35:07: 1000000 INFO @ Wed, 08 Dec 2021 20:35:15: 5000000 INFO @ Wed, 08 Dec 2021 20:35:17: 2000000 INFO @ Wed, 08 Dec 2021 20:35:23: 6000000 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 20:35:26: 3000000 INFO @ Wed, 08 Dec 2021 20:35:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.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 20:35:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:35:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:35:32: 7000000 INFO @ Wed, 08 Dec 2021 20:35:35: 4000000 INFO @ Wed, 08 Dec 2021 20:35:38: 1000000 INFO @ Wed, 08 Dec 2021 20:35:41: 8000000 INFO @ Wed, 08 Dec 2021 20:35:45: 5000000 INFO @ Wed, 08 Dec 2021 20:35:47: 2000000 INFO @ Wed, 08 Dec 2021 20:35:50: 9000000 INFO @ Wed, 08 Dec 2021 20:35:54: 6000000 INFO @ Wed, 08 Dec 2021 20:35:56: 3000000 INFO @ Wed, 08 Dec 2021 20:35:59: 10000000 INFO @ Wed, 08 Dec 2021 20:36:03: 7000000 INFO @ Wed, 08 Dec 2021 20:36:05: 4000000 INFO @ Wed, 08 Dec 2021 20:36:09: 11000000 INFO @ Wed, 08 Dec 2021 20:36:12: 8000000 INFO @ Wed, 08 Dec 2021 20:36:14: 5000000 INFO @ Wed, 08 Dec 2021 20:36:17: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:36:17: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:36:17: #1 total tags in treatment: 11898519 INFO @ Wed, 08 Dec 2021 20:36:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:36:17: #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 20:36:17: #1 tags after filtering in treatment: 11898519 INFO @ Wed, 08 Dec 2021 20:36:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:36:17: #1 finished! INFO @ Wed, 08 Dec 2021 20:36:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:36:18: #2 number of paired peaks: 459 WARNING @ Wed, 08 Dec 2021 20:36:18: 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 @ Wed, 08 Dec 2021 20:36:18: start model_add_line... INFO @ Wed, 08 Dec 2021 20:36:18: start X-correlation... INFO @ Wed, 08 Dec 2021 20:36:18: end of X-cor INFO @ Wed, 08 Dec 2021 20:36:18: #2 finished! INFO @ Wed, 08 Dec 2021 20:36:18: #2 predicted fragment length is 45 bps INFO @ Wed, 08 Dec 2021 20:36:18: #2 alternative fragment length(s) may be 2,45,545,572,598 bps INFO @ Wed, 08 Dec 2021 20:36:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.05_model.r WARNING @ Wed, 08 Dec 2021 20:36:18: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:36:18: #2 You may need to consider one of the other alternative d(s): 2,45,545,572,598 WARNING @ Wed, 08 Dec 2021 20:36:18: #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 20:36:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:36:21: 9000000 INFO @ Wed, 08 Dec 2021 20:36:23: 6000000 INFO @ Wed, 08 Dec 2021 20:36:30: 10000000 INFO @ Wed, 08 Dec 2021 20:36:32: 7000000 INFO @ Wed, 08 Dec 2021 20:36:39: 11000000 INFO @ Wed, 08 Dec 2021 20:36:41: 8000000 INFO @ Wed, 08 Dec 2021 20:36:43: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:36:47: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:36:47: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:36:47: #1 total tags in treatment: 11898519 INFO @ Wed, 08 Dec 2021 20:36:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:36:47: #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 20:36:47: #1 tags after filtering in treatment: 11898519 INFO @ Wed, 08 Dec 2021 20:36:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:36:47: #1 finished! INFO @ Wed, 08 Dec 2021 20:36:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:36:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:36:48: #2 number of paired peaks: 459 WARNING @ Wed, 08 Dec 2021 20:36:48: 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 @ Wed, 08 Dec 2021 20:36:48: start model_add_line... INFO @ Wed, 08 Dec 2021 20:36:48: start X-correlation... INFO @ Wed, 08 Dec 2021 20:36:48: end of X-cor INFO @ Wed, 08 Dec 2021 20:36:48: #2 finished! INFO @ Wed, 08 Dec 2021 20:36:48: #2 predicted fragment length is 45 bps INFO @ Wed, 08 Dec 2021 20:36:48: #2 alternative fragment length(s) may be 2,45,545,572,598 bps INFO @ Wed, 08 Dec 2021 20:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.10_model.r WARNING @ Wed, 08 Dec 2021 20:36:48: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:36:48: #2 You may need to consider one of the other alternative d(s): 2,45,545,572,598 WARNING @ Wed, 08 Dec 2021 20:36:48: #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 20:36:48: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:36:49: 9000000 INFO @ Wed, 08 Dec 2021 20:36:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:36:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:36:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.05_summits.bed INFO @ Wed, 08 Dec 2021 20:36:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (656 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:36:58: 10000000 INFO @ Wed, 08 Dec 2021 20:37:06: 11000000 INFO @ Wed, 08 Dec 2021 20:37:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:37:13: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:37:13: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:37:13: #1 total tags in treatment: 11898519 INFO @ Wed, 08 Dec 2021 20:37:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:37:13: #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 20:37:14: #1 tags after filtering in treatment: 11898519 INFO @ Wed, 08 Dec 2021 20:37:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:37:14: #1 finished! INFO @ Wed, 08 Dec 2021 20:37:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:37:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:37:14: #2 number of paired peaks: 459 WARNING @ Wed, 08 Dec 2021 20:37:14: 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 @ Wed, 08 Dec 2021 20:37:14: start model_add_line... INFO @ Wed, 08 Dec 2021 20:37:15: start X-correlation... INFO @ Wed, 08 Dec 2021 20:37:15: end of X-cor INFO @ Wed, 08 Dec 2021 20:37:15: #2 finished! INFO @ Wed, 08 Dec 2021 20:37:15: #2 predicted fragment length is 45 bps INFO @ Wed, 08 Dec 2021 20:37:15: #2 alternative fragment length(s) may be 2,45,545,572,598 bps INFO @ Wed, 08 Dec 2021 20:37:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.20_model.r WARNING @ Wed, 08 Dec 2021 20:37:15: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:37:15: #2 You may need to consider one of the other alternative d(s): 2,45,545,572,598 WARNING @ Wed, 08 Dec 2021 20:37:15: #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 20:37:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:37:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.10_summits.bed INFO @ Wed, 08 Dec 2021 20:37:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:37:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:37:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:37:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:37:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180802/SRX3180802.20_summits.bed INFO @ Wed, 08 Dec 2021 20:37:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (170 records, 4 fields): 3 millis CompletedMACS2peakCalling