Job ID = 14159384 SRX = SRX3180831 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15884468 spots for SRR6030482/SRR6030482.sra Written 15884468 spots for SRR6030482/SRR6030482.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159587 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:47 15884468 reads; of these: 15884468 (100.00%) were unpaired; of these: 447303 (2.82%) aligned 0 times 12811664 (80.66%) aligned exactly 1 time 2625501 (16.53%) aligned >1 times 97.18% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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] 1539671 / 15437165 = 0.0997 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 21:36:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.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 21:36:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:36:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:36:40: 1000000 INFO @ Wed, 08 Dec 2021 21:36:46: 2000000 INFO @ Wed, 08 Dec 2021 21:36:52: 3000000 INFO @ Wed, 08 Dec 2021 21:36:58: 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 21:37:04: 5000000 INFO @ Wed, 08 Dec 2021 21:37:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.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 21:37:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:37:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:37:10: 6000000 INFO @ Wed, 08 Dec 2021 21:37:11: 1000000 INFO @ Wed, 08 Dec 2021 21:37:16: 7000000 INFO @ Wed, 08 Dec 2021 21:37:17: 2000000 INFO @ Wed, 08 Dec 2021 21:37:23: 8000000 INFO @ Wed, 08 Dec 2021 21:37:23: 3000000 INFO @ Wed, 08 Dec 2021 21:37:29: 9000000 INFO @ Wed, 08 Dec 2021 21:37:29: 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 21:37:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.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 21:37:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:37:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:37:35: 10000000 INFO @ Wed, 08 Dec 2021 21:37:35: 5000000 INFO @ Wed, 08 Dec 2021 21:37:41: 1000000 INFO @ Wed, 08 Dec 2021 21:37:41: 11000000 INFO @ Wed, 08 Dec 2021 21:37:42: 6000000 INFO @ Wed, 08 Dec 2021 21:37:47: 2000000 INFO @ Wed, 08 Dec 2021 21:37:48: 12000000 INFO @ Wed, 08 Dec 2021 21:37:48: 7000000 INFO @ Wed, 08 Dec 2021 21:37:54: 13000000 INFO @ Wed, 08 Dec 2021 21:37:54: 3000000 INFO @ Wed, 08 Dec 2021 21:37:55: 8000000 INFO @ Wed, 08 Dec 2021 21:38:00: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:38:00: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:38:00: #1 total tags in treatment: 13897494 INFO @ Wed, 08 Dec 2021 21:38:00: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:38:00: #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 21:38:00: #1 tags after filtering in treatment: 13897494 INFO @ Wed, 08 Dec 2021 21:38:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:38:00: #1 finished! INFO @ Wed, 08 Dec 2021 21:38:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:38:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:38:00: 4000000 INFO @ Wed, 08 Dec 2021 21:38:01: #2 number of paired peaks: 328 WARNING @ Wed, 08 Dec 2021 21:38:01: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Wed, 08 Dec 2021 21:38:01: start model_add_line... INFO @ Wed, 08 Dec 2021 21:38:01: start X-correlation... INFO @ Wed, 08 Dec 2021 21:38:01: end of X-cor INFO @ Wed, 08 Dec 2021 21:38:01: #2 finished! INFO @ Wed, 08 Dec 2021 21:38:01: #2 predicted fragment length is 46 bps INFO @ Wed, 08 Dec 2021 21:38:01: #2 alternative fragment length(s) may be 2,46,528,569,585 bps INFO @ Wed, 08 Dec 2021 21:38:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.05_model.r WARNING @ Wed, 08 Dec 2021 21:38:01: #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 21:38:01: #2 You may need to consider one of the other alternative d(s): 2,46,528,569,585 WARNING @ Wed, 08 Dec 2021 21:38:01: #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 21:38:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:38:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:38:01: 9000000 INFO @ Wed, 08 Dec 2021 21:38:06: 5000000 INFO @ Wed, 08 Dec 2021 21:38:07: 10000000 INFO @ Wed, 08 Dec 2021 21:38:12: 6000000 INFO @ Wed, 08 Dec 2021 21:38:13: 11000000 INFO @ Wed, 08 Dec 2021 21:38:19: 7000000 INFO @ Wed, 08 Dec 2021 21:38:19: 12000000 INFO @ Wed, 08 Dec 2021 21:38:25: 8000000 INFO @ Wed, 08 Dec 2021 21:38:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:38:25: 13000000 INFO @ Wed, 08 Dec 2021 21:38:31: 9000000 INFO @ Wed, 08 Dec 2021 21:38:31: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:38:31: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:38:31: #1 total tags in treatment: 13897494 INFO @ Wed, 08 Dec 2021 21:38:31: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:38:31: #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 21:38:31: #1 tags after filtering in treatment: 13897494 INFO @ Wed, 08 Dec 2021 21:38:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:38:31: #1 finished! INFO @ Wed, 08 Dec 2021 21:38:31: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:38:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:38:32: #2 number of paired peaks: 328 WARNING @ Wed, 08 Dec 2021 21:38:32: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Wed, 08 Dec 2021 21:38:32: start model_add_line... INFO @ Wed, 08 Dec 2021 21:38:32: start X-correlation... INFO @ Wed, 08 Dec 2021 21:38:32: end of X-cor INFO @ Wed, 08 Dec 2021 21:38:32: #2 finished! INFO @ Wed, 08 Dec 2021 21:38:32: #2 predicted fragment length is 46 bps INFO @ Wed, 08 Dec 2021 21:38:32: #2 alternative fragment length(s) may be 2,46,528,569,585 bps INFO @ Wed, 08 Dec 2021 21:38:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.10_model.r WARNING @ Wed, 08 Dec 2021 21:38:32: #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 21:38:32: #2 You may need to consider one of the other alternative d(s): 2,46,528,569,585 WARNING @ Wed, 08 Dec 2021 21:38:32: #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 21:38:32: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:38:32: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:38:37: 10000000 INFO @ Wed, 08 Dec 2021 21:38:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:38:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:38:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.05_summits.bed INFO @ Wed, 08 Dec 2021 21:38:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (725 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:38:43: 11000000 INFO @ Wed, 08 Dec 2021 21:38:48: 12000000 INFO @ Wed, 08 Dec 2021 21:38:54: 13000000 INFO @ Wed, 08 Dec 2021 21:38:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:38:59: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:38:59: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:38:59: #1 total tags in treatment: 13897494 INFO @ Wed, 08 Dec 2021 21:38:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:38:59: #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 21:39:00: #1 tags after filtering in treatment: 13897494 INFO @ Wed, 08 Dec 2021 21:39:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:39:00: #1 finished! INFO @ Wed, 08 Dec 2021 21:39:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:39:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:39:01: #2 number of paired peaks: 328 WARNING @ Wed, 08 Dec 2021 21:39:01: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Wed, 08 Dec 2021 21:39:01: start model_add_line... INFO @ Wed, 08 Dec 2021 21:39:01: start X-correlation... INFO @ Wed, 08 Dec 2021 21:39:01: end of X-cor INFO @ Wed, 08 Dec 2021 21:39:01: #2 finished! INFO @ Wed, 08 Dec 2021 21:39:01: #2 predicted fragment length is 46 bps INFO @ Wed, 08 Dec 2021 21:39:01: #2 alternative fragment length(s) may be 2,46,528,569,585 bps INFO @ Wed, 08 Dec 2021 21:39:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.20_model.r WARNING @ Wed, 08 Dec 2021 21:39:01: #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 21:39:01: #2 You may need to consider one of the other alternative d(s): 2,46,528,569,585 WARNING @ Wed, 08 Dec 2021 21:39:01: #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 21:39:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:39:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:39:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:39:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:39:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.10_summits.bed INFO @ Wed, 08 Dec 2021 21:39:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:39:26: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:39:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:39:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:39:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180831/SRX3180831.20_summits.bed INFO @ Wed, 08 Dec 2021 21:39:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 1 millis CompletedMACS2peakCalling