Job ID = 12264831 SRX = SRX7687154 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22511278 spots for SRR11034897/SRR11034897.sra Written 22511278 spots for SRR11034897/SRR11034897.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265377 ("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: 00:25:23 22511278 reads; of these: 22511278 (100.00%) were paired; of these: 5883286 (26.13%) aligned concordantly 0 times 14692417 (65.27%) aligned concordantly exactly 1 time 1935575 (8.60%) aligned concordantly >1 times ---- 5883286 pairs aligned concordantly 0 times; of these: 1562337 (26.56%) aligned discordantly 1 time ---- 4320949 pairs aligned 0 times concordantly or discordantly; of these: 8641898 mates make up the pairs; of these: 8083793 (93.54%) aligned 0 times 261995 (3.03%) aligned exactly 1 time 296110 (3.43%) aligned >1 times 82.05% overall alignment rate Time searching: 00:25:24 Overall time: 00:25:24 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 12604781 / 18149113 = 0.6945 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:30:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.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 @ Sat, 03 Apr 2021 06:30:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:30:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:30:19: 1000000 INFO @ Sat, 03 Apr 2021 06:30:27: 2000000 INFO @ Sat, 03 Apr 2021 06:30:35: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:30:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.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 @ Sat, 03 Apr 2021 06:30:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:30:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:30:43: 4000000 INFO @ Sat, 03 Apr 2021 06:30:51: 5000000 INFO @ Sat, 03 Apr 2021 06:30:51: 1000000 INFO @ Sat, 03 Apr 2021 06:30:59: 6000000 INFO @ Sat, 03 Apr 2021 06:31:02: 2000000 INFO @ Sat, 03 Apr 2021 06:31:07: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.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 @ Sat, 03 Apr 2021 06:31:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:31:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:31:13: 3000000 INFO @ Sat, 03 Apr 2021 06:31:15: 8000000 INFO @ Sat, 03 Apr 2021 06:31:21: 1000000 INFO @ Sat, 03 Apr 2021 06:31:23: 9000000 INFO @ Sat, 03 Apr 2021 06:31:24: 4000000 INFO @ Sat, 03 Apr 2021 06:31:31: 10000000 INFO @ Sat, 03 Apr 2021 06:31:32: 2000000 INFO @ Sat, 03 Apr 2021 06:31:34: 5000000 INFO @ Sat, 03 Apr 2021 06:31:39: 11000000 INFO @ Sat, 03 Apr 2021 06:31:42: 3000000 INFO @ Sat, 03 Apr 2021 06:31:44: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:31:44: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:31:44: #1 total tags in treatment: 4970886 INFO @ Sat, 03 Apr 2021 06:31:44: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:31:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:31:44: 6000000 INFO @ Sat, 03 Apr 2021 06:31:44: #1 tags after filtering in treatment: 3850772 INFO @ Sat, 03 Apr 2021 06:31:44: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 06:31:44: #1 finished! INFO @ Sat, 03 Apr 2021 06:31:44: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:31:45: #2 number of paired peaks: 559 WARNING @ Sat, 03 Apr 2021 06:31:45: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sat, 03 Apr 2021 06:31:45: start model_add_line... INFO @ Sat, 03 Apr 2021 06:31:45: start X-correlation... INFO @ Sat, 03 Apr 2021 06:31:45: end of X-cor INFO @ Sat, 03 Apr 2021 06:31:45: #2 finished! INFO @ Sat, 03 Apr 2021 06:31:45: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 06:31:45: #2 alternative fragment length(s) may be 4,146 bps INFO @ Sat, 03 Apr 2021 06:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.05_model.r WARNING @ Sat, 03 Apr 2021 06:31:45: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:31:45: #2 You may need to consider one of the other alternative d(s): 4,146 WARNING @ Sat, 03 Apr 2021 06:31:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:31:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:31:51: 4000000 INFO @ Sat, 03 Apr 2021 06:31:54: 7000000 INFO @ Sat, 03 Apr 2021 06:31:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:32:01: 5000000 INFO @ Sat, 03 Apr 2021 06:32:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:32:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:32:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.05_summits.bed INFO @ Sat, 03 Apr 2021 06:32:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (731 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:32:04: 8000000 INFO @ Sat, 03 Apr 2021 06:32:10: 6000000 INFO @ Sat, 03 Apr 2021 06:32:14: 9000000 INFO @ Sat, 03 Apr 2021 06:32:20: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:32:24: 10000000 INFO @ Sat, 03 Apr 2021 06:32:30: 8000000 INFO @ Sat, 03 Apr 2021 06:32:34: 11000000 INFO @ Sat, 03 Apr 2021 06:32:39: 9000000 INFO @ Sat, 03 Apr 2021 06:32:41: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:32:41: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:32:41: #1 total tags in treatment: 4970886 INFO @ Sat, 03 Apr 2021 06:32:41: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:32:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:32:42: #1 tags after filtering in treatment: 3850772 INFO @ Sat, 03 Apr 2021 06:32:42: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 06:32:42: #1 finished! INFO @ Sat, 03 Apr 2021 06:32:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:32:42: #2 number of paired peaks: 559 WARNING @ Sat, 03 Apr 2021 06:32:42: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sat, 03 Apr 2021 06:32:42: start model_add_line... INFO @ Sat, 03 Apr 2021 06:32:42: start X-correlation... INFO @ Sat, 03 Apr 2021 06:32:42: end of X-cor INFO @ Sat, 03 Apr 2021 06:32:42: #2 finished! INFO @ Sat, 03 Apr 2021 06:32:42: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 06:32:42: #2 alternative fragment length(s) may be 4,146 bps INFO @ Sat, 03 Apr 2021 06:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.10_model.r WARNING @ Sat, 03 Apr 2021 06:32:42: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:32:42: #2 You may need to consider one of the other alternative d(s): 4,146 WARNING @ Sat, 03 Apr 2021 06:32:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:32:42: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:32:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:32:48: 10000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:32:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:32:57: 11000000 INFO @ Sat, 03 Apr 2021 06:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.10_summits.bed INFO @ Sat, 03 Apr 2021 06:33:01: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (371 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:33:03: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:33:03: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:33:03: #1 total tags in treatment: 4970886 INFO @ Sat, 03 Apr 2021 06:33:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:33:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:33:03: #1 tags after filtering in treatment: 3850772 INFO @ Sat, 03 Apr 2021 06:33:03: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 06:33:03: #1 finished! INFO @ Sat, 03 Apr 2021 06:33:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:33:03: #2 number of paired peaks: 559 WARNING @ Sat, 03 Apr 2021 06:33:03: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sat, 03 Apr 2021 06:33:03: start model_add_line... INFO @ Sat, 03 Apr 2021 06:33:03: start X-correlation... INFO @ Sat, 03 Apr 2021 06:33:03: end of X-cor INFO @ Sat, 03 Apr 2021 06:33:03: #2 finished! INFO @ Sat, 03 Apr 2021 06:33:03: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 06:33:03: #2 alternative fragment length(s) may be 4,146 bps INFO @ Sat, 03 Apr 2021 06:33:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.20_model.r WARNING @ Sat, 03 Apr 2021 06:33:03: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:33:03: #2 You may need to consider one of the other alternative d(s): 4,146 WARNING @ Sat, 03 Apr 2021 06:33:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:33:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:33:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:33:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:33:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:33:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687154/SRX7687154.20_summits.bed INFO @ Sat, 03 Apr 2021 06:33:22: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (149 records, 4 fields): 3 millis CompletedMACS2peakCalling