[2023-03-16 15:45:05,543] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:45:05,543] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:45:05,544] [INFO] DQC Reference Directory: /var/lib/cwl/stga88a1d89-4c4f-43fd-973e-7270d0746683/dqc_reference
[2023-03-16 15:45:06,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:45:06,886] [INFO] Task started: Prodigal
[2023-03-16 15:45:06,886] [INFO] Running command: cat /var/lib/cwl/stgf2554e04-efb2-45e9-8019-cbc9674b4705/OceanDNA-b27556.fa | prodigal -d OceanDNA-b27556/cds.fna -a OceanDNA-b27556/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:45:28,442] [INFO] Task succeeded: Prodigal
[2023-03-16 15:45:28,442] [INFO] Task started: HMMsearch
[2023-03-16 15:45:28,442] [INFO] Running command: hmmsearch --tblout OceanDNA-b27556/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga88a1d89-4c4f-43fd-973e-7270d0746683/dqc_reference/reference_markers.hmm OceanDNA-b27556/protein.faa > /dev/null
[2023-03-16 15:45:28,624] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:45:28,625] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf2554e04-efb2-45e9-8019-cbc9674b4705/OceanDNA-b27556.fa]
[2023-03-16 15:45:28,644] [INFO] Query marker FASTA was written to OceanDNA-b27556/markers.fasta
[2023-03-16 15:45:28,646] [INFO] Task started: Blastn
[2023-03-16 15:45:28,646] [INFO] Running command: blastn -query OceanDNA-b27556/markers.fasta -db /var/lib/cwl/stga88a1d89-4c4f-43fd-973e-7270d0746683/dqc_reference/reference_markers.fasta -out OceanDNA-b27556/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:45:29,908] [INFO] Task succeeded: Blastn
[2023-03-16 15:45:29,909] [INFO] Selected 22 target genomes.
[2023-03-16 15:45:29,909] [INFO] Target genome list was writen to OceanDNA-b27556/target_genomes.txt
[2023-03-16 15:45:29,922] [INFO] Task started: fastANI
[2023-03-16 15:45:29,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2554e04-efb2-45e9-8019-cbc9674b4705/OceanDNA-b27556.fa --refList OceanDNA-b27556/target_genomes.txt --output OceanDNA-b27556/fastani_result.tsv --threads 1
[2023-03-16 15:45:53,333] [INFO] Task succeeded: fastANI
[2023-03-16 15:45:53,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga88a1d89-4c4f-43fd-973e-7270d0746683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:45:53,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga88a1d89-4c4f-43fd-973e-7270d0746683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:45:53,400] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:45:53,400] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 15:45:53,400] [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
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	76.7105	200	997	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	76.6745	172	997	95	below_threshold
Ruegeria profundi	strain=ZGT108	GCA_001507545.1	1685378	1685378	type	True	76.6545	122	997	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	76.5976	162	997	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	76.4957	153	997	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	76.4882	171	997	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.4685	182	997	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.461	143	997	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	76.3678	127	997	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.3673	158	997	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	76.3663	127	997	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	76.3278	122	997	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.3009	145	997	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.2638	112	997	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	76.2602	156	997	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	76.2593	91	997	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	76.2586	91	997	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	76.2466	116	997	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	76.2122	138	997	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	76.1654	158	997	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	76.158	159	997	95	below_threshold
Litoreibacter janthinus	strain=DSM 26921	GCA_900111945.1	670154	670154	type	True	75.8422	89	997	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 15:45:53,400] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27556/tc_result.tsv
[2023-03-16 15:45:53,400] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:45:53,400] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:45:53,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga88a1d89-4c4f-43fd-973e-7270d0746683/dqc_reference/checkm_data
[2023-03-16 15:45:53,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:45:53,406] [INFO] Task started: CheckM
[2023-03-16 15:45:53,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27556/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27556/checkm_input OceanDNA-b27556/checkm_result
[2023-03-16 15:46:58,772] [INFO] Task succeeded: CheckM
[2023-03-16 15:46:58,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:46:58,775] [INFO] ===== Completeness check finished =====
[2023-03-16 15:46:58,775] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:46:58,775] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27556/markers.fasta)
[2023-03-16 15:46:58,777] [INFO] Task started: Blastn
[2023-03-16 15:46:58,777] [INFO] Running command: blastn -query OceanDNA-b27556/markers.fasta -db /var/lib/cwl/stga88a1d89-4c4f-43fd-973e-7270d0746683/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27556/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:47:00,582] [INFO] Task succeeded: Blastn
[2023-03-16 15:47:00,583] [INFO] Selected 22 target genomes.
[2023-03-16 15:47:00,583] [INFO] Target genome list was writen to OceanDNA-b27556/target_genomes_gtdb.txt
[2023-03-16 15:47:01,040] [INFO] Task started: fastANI
[2023-03-16 15:47:01,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2554e04-efb2-45e9-8019-cbc9674b4705/OceanDNA-b27556.fa --refList OceanDNA-b27556/target_genomes_gtdb.txt --output OceanDNA-b27556/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:47:15,366] [INFO] Task succeeded: fastANI
[2023-03-16 15:47:15,378] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 15:47:15,378] [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_013214665.1	s__JABSSA01 sp013214665	77.6589	311	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABSSA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214715.1	s__JABSSB01 sp013214715	76.7239	145	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABSSB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	76.7105	200	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013033515.1	s__Ruegeria sp013033515	76.627	145	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.60	97.60	0.95	0.93	6	-
GCF_001507595.1	s__Ruegeria marisrubri	76.6101	160	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.5823	182	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCA_000158135.1	s__Ruegeria sp000158135	76.5546	133	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401465.1	s__Aestuariivita sp018401465	76.5456	151	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216475.1	s__GCA-004216475 sp004216475	76.5047	169	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-004216475	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803475.1	s__Aliishimia ponticola	76.4782	180	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	76.4734	151	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	76.425	177	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_000814005.1	s__Ruegeria sp000814005	76.4095	138	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	76.3296	138	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	76.3009	145	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006064855.1	s__Sulfitobacter sp006064855	76.2826	114	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	76.2721	155	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_002407245.1	s__Phaeobacter piscinae	76.2254	137	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCA_003511785.1	s__UBA7951 sp003511785	76.2193	111	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834145.1	s__Roseovarius salinarum	76.2162	74	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	76.2081	151	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731875.1	s__Sulfitobacter sp002731875	75.9092	101	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.91	99.88	0.91	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-16 15:47:15,378] [INFO] GTDB search result was written to OceanDNA-b27556/result_gtdb.tsv
[2023-03-16 15:47:15,378] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:47:15,381] [INFO] DFAST_QC result json was written to OceanDNA-b27556/dqc_result.json
[2023-03-16 15:47:15,381] [INFO] DFAST_QC completed!
[2023-03-16 15:47:15,381] [INFO] Total running time: 0h2m10s