[2023-03-17 01:23:45,118] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:23:45,118] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:23:45,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg1023c98c-691f-4f10-860f-8ea32eba583d/dqc_reference
[2023-03-17 01:23:46,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:23:46,317] [INFO] Task started: Prodigal
[2023-03-17 01:23:46,318] [INFO] Running command: cat /var/lib/cwl/stgbf02b715-c2c9-44e5-86e5-df29902aa741/OceanDNA-b29510.fa | prodigal -d OceanDNA-b29510/cds.fna -a OceanDNA-b29510/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:24:04,203] [INFO] Task succeeded: Prodigal
[2023-03-17 01:24:04,203] [INFO] Task started: HMMsearch
[2023-03-17 01:24:04,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b29510/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1023c98c-691f-4f10-860f-8ea32eba583d/dqc_reference/reference_markers.hmm OceanDNA-b29510/protein.faa > /dev/null
[2023-03-17 01:24:04,379] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:24:04,380] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbf02b715-c2c9-44e5-86e5-df29902aa741/OceanDNA-b29510.fa]
[2023-03-17 01:24:04,402] [INFO] Query marker FASTA was written to OceanDNA-b29510/markers.fasta
[2023-03-17 01:24:04,403] [INFO] Task started: Blastn
[2023-03-17 01:24:04,403] [INFO] Running command: blastn -query OceanDNA-b29510/markers.fasta -db /var/lib/cwl/stg1023c98c-691f-4f10-860f-8ea32eba583d/dqc_reference/reference_markers.fasta -out OceanDNA-b29510/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:05,157] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:05,158] [INFO] Selected 30 target genomes.
[2023-03-17 01:24:05,158] [INFO] Target genome list was writen to OceanDNA-b29510/target_genomes.txt
[2023-03-17 01:24:05,175] [INFO] Task started: fastANI
[2023-03-17 01:24:05,175] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf02b715-c2c9-44e5-86e5-df29902aa741/OceanDNA-b29510.fa --refList OceanDNA-b29510/target_genomes.txt --output OceanDNA-b29510/fastani_result.tsv --threads 1
[2023-03-17 01:24:26,682] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:26,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1023c98c-691f-4f10-860f-8ea32eba583d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:24:26,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1023c98c-691f-4f10-860f-8ea32eba583d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:24:26,698] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:24:26,698] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:24:26,699] [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
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.2115	322	904	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.1907	354	904	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.1879	332	904	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.1717	356	904	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.1459	341	904	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.114	310	904	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.9373	339	904	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	77.8684	301	904	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.7579	303	904	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.7273	265	904	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.7218	286	904	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	77.6834	318	904	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	77.6694	265	904	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	77.5576	253	904	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	77.523	263	904	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.5198	212	904	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	77.4925	280	904	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	77.4797	260	904	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	77.4729	259	904	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.4719	271	904	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.4628	265	904	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.4182	268	904	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	77.403	294	904	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	77.3072	230	904	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.2605	244	904	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	77.0227	212	904	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8383	205	904	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	76.8063	168	904	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	76.7804	224	904	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	76.7022	143	904	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:24:26,699] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29510/tc_result.tsv
[2023-03-17 01:24:26,699] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:24:26,699] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:24:26,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1023c98c-691f-4f10-860f-8ea32eba583d/dqc_reference/checkm_data
[2023-03-17 01:24:26,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:24:26,753] [INFO] Task started: CheckM
[2023-03-17 01:24:26,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29510/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29510/checkm_input OceanDNA-b29510/checkm_result
[2023-03-17 01:25:13,654] [INFO] Task succeeded: CheckM
[2023-03-17 01:25:13,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:25:13,656] [INFO] ===== Completeness check finished =====
[2023-03-17 01:25:13,657] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:25:13,657] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29510/markers.fasta)
[2023-03-17 01:25:13,657] [INFO] Task started: Blastn
[2023-03-17 01:25:13,657] [INFO] Running command: blastn -query OceanDNA-b29510/markers.fasta -db /var/lib/cwl/stg1023c98c-691f-4f10-860f-8ea32eba583d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29510/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:25:14,996] [INFO] Task succeeded: Blastn
[2023-03-17 01:25:14,997] [INFO] Selected 28 target genomes.
[2023-03-17 01:25:14,997] [INFO] Target genome list was writen to OceanDNA-b29510/target_genomes_gtdb.txt
[2023-03-17 01:25:15,328] [INFO] Task started: fastANI
[2023-03-17 01:25:15,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf02b715-c2c9-44e5-86e5-df29902aa741/OceanDNA-b29510.fa --refList OceanDNA-b29510/target_genomes_gtdb.txt --output OceanDNA-b29510/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:25:37,271] [INFO] Task succeeded: fastANI
[2023-03-17 01:25:37,287] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:25:37,287] [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_006226775.1	s__Marinovum sp006226775	79.7039	488	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	79.2638	503	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_001975705.1	s__Salipiger abyssi	78.3111	344	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.208	335	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.2004	323	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	78.0909	312	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	77.8774	299	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	77.8249	318	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009762325.1	s__Roseovarius faecimaris	77.7805	314	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806385.1	s__Epibacterium sp011806385	77.7472	284	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	77.7395	306	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_005434965.1	s__Marimonas lutisalis	77.7354	290	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	77.7218	286	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	77.7151	266	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	77.6734	319	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	77.6667	278	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_008369105.1	s__Aquicoccus porphyridii	77.5828	265	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009363255.1	s__Roseivivax sp009363255	77.566	271	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	99.55	99.55	0.94	0.94	2	-
GCF_900172365.1	s__Roseovarius gaetbuli	77.545	254	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389685.1	s__Aquicoccus sp011389685	77.5435	248	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	77.5198	212	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	77.5145	269	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259905.1	s__Salipiger aestuarii	77.4919	259	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.58	99.38	0.94	0.92	5	-
GCF_900102075.1	s__Salipiger thiooxidans	77.4725	271	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_000169415.1	s__Sagittula stellata	77.3783	240	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363615.1	s__Ruegeria sp009363615	77.2218	238	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.20	96.03	0.88	0.85	16	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	76.8794	229	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	76.7804	224	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:25:37,287] [INFO] GTDB search result was written to OceanDNA-b29510/result_gtdb.tsv
[2023-03-17 01:25:37,287] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:25:37,290] [INFO] DFAST_QC result json was written to OceanDNA-b29510/dqc_result.json
[2023-03-17 01:25:37,290] [INFO] DFAST_QC completed!
[2023-03-17 01:25:37,290] [INFO] Total running time: 0h1m52s