[2023-03-16 07:34:40,565] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:34:40,565] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:34:40,565] [INFO] DQC Reference Directory: /var/lib/cwl/stgd532723e-85e2-4915-af23-44142a212919/dqc_reference
[2023-03-16 07:34:42,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:34:42,228] [INFO] Task started: Prodigal
[2023-03-16 07:34:42,228] [INFO] Running command: cat /var/lib/cwl/stg5bfe6e5c-c5c1-4277-ae23-e58ccf18f592/OceanDNA-b35890.fa | prodigal -d OceanDNA-b35890/cds.fna -a OceanDNA-b35890/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:35:08,089] [INFO] Task succeeded: Prodigal
[2023-03-16 07:35:08,089] [INFO] Task started: HMMsearch
[2023-03-16 07:35:08,089] [INFO] Running command: hmmsearch --tblout OceanDNA-b35890/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd532723e-85e2-4915-af23-44142a212919/dqc_reference/reference_markers.hmm OceanDNA-b35890/protein.faa > /dev/null
[2023-03-16 07:35:08,309] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:35:08,310] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5bfe6e5c-c5c1-4277-ae23-e58ccf18f592/OceanDNA-b35890.fa]
[2023-03-16 07:35:08,344] [INFO] Query marker FASTA was written to OceanDNA-b35890/markers.fasta
[2023-03-16 07:35:08,344] [INFO] Task started: Blastn
[2023-03-16 07:35:08,344] [INFO] Running command: blastn -query OceanDNA-b35890/markers.fasta -db /var/lib/cwl/stgd532723e-85e2-4915-af23-44142a212919/dqc_reference/reference_markers.fasta -out OceanDNA-b35890/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:35:09,092] [INFO] Task succeeded: Blastn
[2023-03-16 07:35:09,095] [INFO] Selected 29 target genomes.
[2023-03-16 07:35:09,095] [INFO] Target genome list was writen to OceanDNA-b35890/target_genomes.txt
[2023-03-16 07:35:09,235] [INFO] Task started: fastANI
[2023-03-16 07:35:09,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bfe6e5c-c5c1-4277-ae23-e58ccf18f592/OceanDNA-b35890.fa --refList OceanDNA-b35890/target_genomes.txt --output OceanDNA-b35890/fastani_result.tsv --threads 1
[2023-03-16 07:35:27,472] [INFO] Task succeeded: fastANI
[2023-03-16 07:35:27,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd532723e-85e2-4915-af23-44142a212919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:35:27,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd532723e-85e2-4915-af23-44142a212919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:35:27,489] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:35:27,489] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:35:27,489] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.0817	271	1446	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.0726	94	1446	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.0725	138	1446	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.054	148	1446	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	75.9744	111	1446	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	75.9208	171	1446	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	75.9096	102	1446	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.8883	151	1446	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	75.8648	153	1446	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	75.8504	127	1446	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.8002	155	1446	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	75.7711	109	1446	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	75.7312	163	1446	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	75.728	104	1446	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.7192	150	1446	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	75.7176	165	1446	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	75.717	117	1446	95	below_threshold
Halofilum ochraceum	strain=XJ16	GCA_001614315.2	1611323	1611323	type	True	75.7076	100	1446	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	75.6987	119	1446	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.6436	172	1446	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.6349	155	1446	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	75.6242	130	1446	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.597	129	1446	95	below_threshold
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	75.5733	100	1446	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	75.5567	209	1446	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	75.5435	205	1446	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	75.5306	123	1446	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	75.4684	185	1446	95	below_threshold
Granulosicoccus antarcticus	strain=IMCC3135	GCA_002215215.1	437505	437505	type	True	75.3725	56	1446	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:35:27,489] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35890/tc_result.tsv
[2023-03-16 07:35:27,489] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:35:27,489] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:35:27,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd532723e-85e2-4915-af23-44142a212919/dqc_reference/checkm_data
[2023-03-16 07:35:27,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:35:27,497] [INFO] Task started: CheckM
[2023-03-16 07:35:27,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35890/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35890/checkm_input OceanDNA-b35890/checkm_result
[2023-03-16 07:36:43,529] [INFO] Task succeeded: CheckM
[2023-03-16 07:36:43,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:36:43,571] [INFO] ===== Completeness check finished =====
[2023-03-16 07:36:43,572] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:36:43,572] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35890/markers.fasta)
[2023-03-16 07:36:43,573] [INFO] Task started: Blastn
[2023-03-16 07:36:43,573] [INFO] Running command: blastn -query OceanDNA-b35890/markers.fasta -db /var/lib/cwl/stgd532723e-85e2-4915-af23-44142a212919/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35890/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:36:44,968] [INFO] Task succeeded: Blastn
[2023-03-16 07:36:44,969] [INFO] Selected 26 target genomes.
[2023-03-16 07:36:44,969] [INFO] Target genome list was writen to OceanDNA-b35890/target_genomes_gtdb.txt
[2023-03-16 07:36:45,754] [INFO] Task started: fastANI
[2023-03-16 07:36:45,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bfe6e5c-c5c1-4277-ae23-e58ccf18f592/OceanDNA-b35890.fa --refList OceanDNA-b35890/target_genomes_gtdb.txt --output OceanDNA-b35890/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:36:59,970] [INFO] Task succeeded: fastANI
[2023-03-16 07:36:59,983] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:36:59,983] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002746645.1	s__Granulosicoccus sp002746645	77.0934	180	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Granulosicoccales;f__Granulosicoccaceae;g__Granulosicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.3382	127	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	76.2587	87	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_015494335.1	s__S144-22 sp015494335	76.1628	68	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__S144-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	76.157	71	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001697225.1	s__Immundisolibacter cernigliae	76.0955	95	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	76.0815	271	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.0198	231	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_014359565.1	s__Immundisolibacter sp014359565	75.9454	106	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046015.1	s__SpSt-1174 sp011046015	75.8737	84	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695825.1	s__J048 sp003695825	75.8567	95	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923475.1	s__UBA964 sp009923475	75.8215	97	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	75.7803	121	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182895.1	s__Frateuria_B defendens	75.7515	152	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339665.1	s__Azotobacter chroococcum	75.7312	163	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
GCF_017837635.1	s__Frateuria_A sp017837635	75.728	104	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197755.1	s__Rhodocyclus tenuis	75.6769	121	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	98.79	97.58	0.96	0.93	3	-
GCF_000953855.2	s__Mizugakiibacter sediminis	75.6262	167	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016615815.1	s__Luteimonas sp016615815	75.6085	124	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.14	98.29	0.98	0.95	3	-
GCA_013002205.1	s__Granulosicoccus sp013002205	75.5637	81	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Granulosicoccales;f__Granulosicoccaceae;g__Granulosicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026885.1	s__Azonexus sp012026885	75.4938	104	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464935.1	s__Ga0077536 sp001464935	75.4872	127	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241385.1	s__Dokdonella denitrificans_A	75.4618	216	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:36:59,984] [INFO] GTDB search result was written to OceanDNA-b35890/result_gtdb.tsv
[2023-03-16 07:36:59,984] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:36:59,986] [INFO] DFAST_QC result json was written to OceanDNA-b35890/dqc_result.json
[2023-03-16 07:36:59,986] [INFO] DFAST_QC completed!
[2023-03-16 07:36:59,986] [INFO] Total running time: 0h2m19s