Job ID = 5720785 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:24:20 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T16:32:04 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T16:32:04 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T16:32:04 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T16:32:04 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T16:50:10 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T16:51:13 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 25,175,914 reads read : 50,351,828 reads written : 50,351,828 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 02:22:39 25175914 reads; of these: 25175914 (100.00%) were paired; of these: 6915943 (27.47%) aligned concordantly 0 times 6286601 (24.97%) aligned concordantly exactly 1 time 11973370 (47.56%) aligned concordantly >1 times ---- 6915943 pairs aligned concordantly 0 times; of these: 1004079 (14.52%) aligned discordantly 1 time ---- 5911864 pairs aligned 0 times concordantly or discordantly; of these: 11823728 mates make up the pairs; of these: 4114897 (34.80%) aligned 0 times 1110037 (9.39%) aligned exactly 1 time 6598794 (55.81%) aligned >1 times 91.83% overall alignment rate Time searching: 02:22:39 Overall time: 02:22:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2720968 / 19164207 = 0.1420 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 04:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 04:33:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:33:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:33:12: 1000000 INFO @ Thu, 16 Apr 2020 04:33:19: 2000000 INFO @ Thu, 16 Apr 2020 04:33:26: 3000000 INFO @ Thu, 16 Apr 2020 04:33:33: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 04:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 04:33:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:33:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:33:41: 5000000 INFO @ Thu, 16 Apr 2020 04:33:42: 1000000 INFO @ Thu, 16 Apr 2020 04:33:48: 6000000 INFO @ Thu, 16 Apr 2020 04:33:48: 2000000 INFO @ Thu, 16 Apr 2020 04:33:55: 3000000 INFO @ Thu, 16 Apr 2020 04:33:55: 7000000 INFO @ Thu, 16 Apr 2020 04:34:01: 4000000 INFO @ Thu, 16 Apr 2020 04:34:03: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 04:34:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 04:34:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:34:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:34:07: 5000000 INFO @ Thu, 16 Apr 2020 04:34:10: 9000000 INFO @ Thu, 16 Apr 2020 04:34:12: 1000000 INFO @ Thu, 16 Apr 2020 04:34:14: 6000000 INFO @ Thu, 16 Apr 2020 04:34:17: 10000000 INFO @ Thu, 16 Apr 2020 04:34:18: 2000000 INFO @ Thu, 16 Apr 2020 04:34:20: 7000000 INFO @ Thu, 16 Apr 2020 04:34:24: 3000000 INFO @ Thu, 16 Apr 2020 04:34:25: 11000000 INFO @ Thu, 16 Apr 2020 04:34:27: 8000000 INFO @ Thu, 16 Apr 2020 04:34:31: 4000000 INFO @ Thu, 16 Apr 2020 04:34:31: 12000000 INFO @ Thu, 16 Apr 2020 04:34:33: 9000000 INFO @ Thu, 16 Apr 2020 04:34:37: 5000000 INFO @ Thu, 16 Apr 2020 04:34:39: 13000000 INFO @ Thu, 16 Apr 2020 04:34:39: 10000000 INFO @ Thu, 16 Apr 2020 04:34:43: 6000000 INFO @ Thu, 16 Apr 2020 04:34:46: 11000000 INFO @ Thu, 16 Apr 2020 04:34:46: 14000000 INFO @ Thu, 16 Apr 2020 04:34:50: 7000000 INFO @ Thu, 16 Apr 2020 04:34:53: 12000000 INFO @ Thu, 16 Apr 2020 04:34:54: 15000000 INFO @ Thu, 16 Apr 2020 04:34:56: 8000000 INFO @ Thu, 16 Apr 2020 04:34:59: 13000000 INFO @ Thu, 16 Apr 2020 04:35:01: 16000000 INFO @ Thu, 16 Apr 2020 04:35:02: 9000000 INFO @ Thu, 16 Apr 2020 04:35:05: 14000000 INFO @ Thu, 16 Apr 2020 04:35:08: 17000000 INFO @ Thu, 16 Apr 2020 04:35:09: 10000000 INFO @ Thu, 16 Apr 2020 04:35:12: 15000000 INFO @ Thu, 16 Apr 2020 04:35:15: 11000000 INFO @ Thu, 16 Apr 2020 04:35:16: 18000000 INFO @ Thu, 16 Apr 2020 04:35:18: 16000000 INFO @ Thu, 16 Apr 2020 04:35:22: 12000000 INFO @ Thu, 16 Apr 2020 04:35:23: 19000000 INFO @ Thu, 16 Apr 2020 04:35:24: 17000000 INFO @ Thu, 16 Apr 2020 04:35:28: 13000000 INFO @ Thu, 16 Apr 2020 04:35:31: 20000000 INFO @ Thu, 16 Apr 2020 04:35:31: 18000000 INFO @ Thu, 16 Apr 2020 04:35:35: 14000000 INFO @ Thu, 16 Apr 2020 04:35:37: 19000000 INFO @ Thu, 16 Apr 2020 04:35:38: 21000000 INFO @ Thu, 16 Apr 2020 04:35:41: 15000000 INFO @ Thu, 16 Apr 2020 04:35:44: 20000000 INFO @ Thu, 16 Apr 2020 04:35:46: 22000000 INFO @ Thu, 16 Apr 2020 04:35:47: 16000000 INFO @ Thu, 16 Apr 2020 04:35:50: 21000000 INFO @ Thu, 16 Apr 2020 04:35:53: 23000000 INFO @ Thu, 16 Apr 2020 04:35:54: 17000000 INFO @ Thu, 16 Apr 2020 04:35:57: 22000000 INFO @ Thu, 16 Apr 2020 04:36:00: 18000000 INFO @ Thu, 16 Apr 2020 04:36:00: 24000000 INFO @ Thu, 16 Apr 2020 04:36:03: 23000000 INFO @ Thu, 16 Apr 2020 04:36:06: 19000000 INFO @ Thu, 16 Apr 2020 04:36:08: 25000000 INFO @ Thu, 16 Apr 2020 04:36:10: 24000000 INFO @ Thu, 16 Apr 2020 04:36:13: 20000000 INFO @ Thu, 16 Apr 2020 04:36:15: 26000000 INFO @ Thu, 16 Apr 2020 04:36:16: 25000000 INFO @ Thu, 16 Apr 2020 04:36:19: 21000000 INFO @ Thu, 16 Apr 2020 04:36:22: 26000000 INFO @ Thu, 16 Apr 2020 04:36:23: 27000000 INFO @ Thu, 16 Apr 2020 04:36:26: 22000000 INFO @ Thu, 16 Apr 2020 04:36:29: 27000000 INFO @ Thu, 16 Apr 2020 04:36:30: 28000000 INFO @ Thu, 16 Apr 2020 04:36:32: 23000000 INFO @ Thu, 16 Apr 2020 04:36:35: 28000000 INFO @ Thu, 16 Apr 2020 04:36:38: 29000000 INFO @ Thu, 16 Apr 2020 04:36:38: 24000000 INFO @ Thu, 16 Apr 2020 04:36:41: 29000000 INFO @ Thu, 16 Apr 2020 04:36:45: 25000000 INFO @ Thu, 16 Apr 2020 04:36:45: 30000000 INFO @ Thu, 16 Apr 2020 04:36:48: 30000000 INFO @ Thu, 16 Apr 2020 04:36:51: 26000000 INFO @ Thu, 16 Apr 2020 04:36:52: 31000000 INFO @ Thu, 16 Apr 2020 04:36:54: 31000000 INFO @ Thu, 16 Apr 2020 04:36:58: 27000000 INFO @ Thu, 16 Apr 2020 04:37:00: 32000000 INFO @ Thu, 16 Apr 2020 04:37:01: 32000000 INFO @ Thu, 16 Apr 2020 04:37:04: 28000000 INFO @ Thu, 16 Apr 2020 04:37:07: 33000000 INFO @ Thu, 16 Apr 2020 04:37:08: 33000000 INFO @ Thu, 16 Apr 2020 04:37:10: 29000000 INFO @ Thu, 16 Apr 2020 04:37:14: 34000000 INFO @ Thu, 16 Apr 2020 04:37:15: 34000000 INFO @ Thu, 16 Apr 2020 04:37:17: 30000000 INFO @ Thu, 16 Apr 2020 04:37:22: 35000000 INFO @ Thu, 16 Apr 2020 04:37:22: 35000000 INFO @ Thu, 16 Apr 2020 04:37:23: 31000000 INFO @ Thu, 16 Apr 2020 04:37:29: 32000000 INFO @ Thu, 16 Apr 2020 04:37:29: 36000000 INFO @ Thu, 16 Apr 2020 04:37:30: 36000000 INFO @ Thu, 16 Apr 2020 04:37:36: 33000000 INFO @ Thu, 16 Apr 2020 04:37:36: 37000000 INFO @ Thu, 16 Apr 2020 04:37:37: 37000000 INFO @ Thu, 16 Apr 2020 04:37:42: 34000000 INFO @ Thu, 16 Apr 2020 04:37:44: 38000000 INFO @ Thu, 16 Apr 2020 04:37:44: 38000000 INFO @ Thu, 16 Apr 2020 04:37:48: 35000000 INFO @ Thu, 16 Apr 2020 04:37:51: 39000000 INFO @ Thu, 16 Apr 2020 04:37:52: 39000000 INFO @ Thu, 16 Apr 2020 04:37:54: 36000000 INFO @ Thu, 16 Apr 2020 04:37:59: 40000000 INFO @ Thu, 16 Apr 2020 04:37:59: 40000000 INFO @ Thu, 16 Apr 2020 04:38:01: 37000000 INFO @ Thu, 16 Apr 2020 04:38:05: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:38:05: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:38:05: #1 total tags in treatment: 15669026 INFO @ Thu, 16 Apr 2020 04:38:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:38:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:38:05: #1 tags after filtering in treatment: 13312669 INFO @ Thu, 16 Apr 2020 04:38:05: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:38:05: #1 finished! INFO @ Thu, 16 Apr 2020 04:38:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:38:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:38:06: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:38:06: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:38:06: #1 total tags in treatment: 15669026 INFO @ Thu, 16 Apr 2020 04:38:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:38:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:38:06: #1 tags after filtering in treatment: 13312669 INFO @ Thu, 16 Apr 2020 04:38:06: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:38:06: #1 finished! INFO @ Thu, 16 Apr 2020 04:38:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:38:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:38:06: #2 number of paired peaks: 2956 INFO @ Thu, 16 Apr 2020 04:38:06: start model_add_line... INFO @ Thu, 16 Apr 2020 04:38:06: start X-correlation... INFO @ Thu, 16 Apr 2020 04:38:06: end of X-cor INFO @ Thu, 16 Apr 2020 04:38:06: #2 finished! INFO @ Thu, 16 Apr 2020 04:38:06: #2 predicted fragment length is 227 bps INFO @ Thu, 16 Apr 2020 04:38:06: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 16 Apr 2020 04:38:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.05_model.r INFO @ Thu, 16 Apr 2020 04:38:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:38:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:38:07: #2 number of paired peaks: 2956 INFO @ Thu, 16 Apr 2020 04:38:07: start model_add_line... INFO @ Thu, 16 Apr 2020 04:38:07: start X-correlation... INFO @ Thu, 16 Apr 2020 04:38:07: end of X-cor INFO @ Thu, 16 Apr 2020 04:38:07: #2 finished! INFO @ Thu, 16 Apr 2020 04:38:07: #2 predicted fragment length is 227 bps INFO @ Thu, 16 Apr 2020 04:38:07: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 16 Apr 2020 04:38:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.10_model.r INFO @ Thu, 16 Apr 2020 04:38:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:38:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:38:07: 38000000 INFO @ Thu, 16 Apr 2020 04:38:13: 39000000 INFO @ Thu, 16 Apr 2020 04:38:19: 40000000 INFO @ Thu, 16 Apr 2020 04:38:24: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:38:24: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:38:24: #1 total tags in treatment: 15669026 INFO @ Thu, 16 Apr 2020 04:38:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:38:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:38:24: #1 tags after filtering in treatment: 13312669 INFO @ Thu, 16 Apr 2020 04:38:24: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:38:24: #1 finished! INFO @ Thu, 16 Apr 2020 04:38:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:38:25: #2 number of paired peaks: 2956 INFO @ Thu, 16 Apr 2020 04:38:25: start model_add_line... INFO @ Thu, 16 Apr 2020 04:38:25: start X-correlation... INFO @ Thu, 16 Apr 2020 04:38:26: end of X-cor INFO @ Thu, 16 Apr 2020 04:38:26: #2 finished! INFO @ Thu, 16 Apr 2020 04:38:26: #2 predicted fragment length is 227 bps INFO @ Thu, 16 Apr 2020 04:38:26: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 16 Apr 2020 04:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.20_model.r INFO @ Thu, 16 Apr 2020 04:38:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:38:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:38:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:38:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:38:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:38:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.05_summits.bed INFO @ Thu, 16 Apr 2020 04:38:57: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (15148 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:38:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:38:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:38:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:38:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.10_summits.bed INFO @ Thu, 16 Apr 2020 04:38:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10213 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:39:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246878/SRX5246878.20_summits.bed INFO @ Thu, 16 Apr 2020 04:39:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5728 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。