[2023-03-18 20:13:32,795] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,796] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c53e468-a120-4832-9284-022c84abb904/dqc_reference
[2023-03-18 20:13:34,556] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:34,556] [INFO] Task started: Prodigal
[2023-03-18 20:13:34,557] [INFO] Running command: cat /var/lib/cwl/stgef244568-12f4-4c9f-b0a1-cc1c1e156623/OceanDNA-b30427.fa | prodigal -d OceanDNA-b30427/cds.fna -a OceanDNA-b30427/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:55,844] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:55,845] [INFO] Task started: HMMsearch
[2023-03-18 20:13:55,845] [INFO] Running command: hmmsearch --tblout OceanDNA-b30427/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c53e468-a120-4832-9284-022c84abb904/dqc_reference/reference_markers.hmm OceanDNA-b30427/protein.faa > /dev/null
[2023-03-18 20:13:56,053] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:56,054] [INFO] Found 6/6 markers.
[2023-03-18 20:13:56,076] [INFO] Query marker FASTA was written to OceanDNA-b30427/markers.fasta
[2023-03-18 20:13:56,077] [INFO] Task started: Blastn
[2023-03-18 20:13:56,077] [INFO] Running command: blastn -query OceanDNA-b30427/markers.fasta -db /var/lib/cwl/stg3c53e468-a120-4832-9284-022c84abb904/dqc_reference/reference_markers.fasta -out OceanDNA-b30427/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:56,775] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:56,776] [INFO] Selected 22 target genomes.
[2023-03-18 20:13:56,776] [INFO] Target genome list was writen to OceanDNA-b30427/target_genomes.txt
[2023-03-18 20:13:56,788] [INFO] Task started: fastANI
[2023-03-18 20:13:56,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgef244568-12f4-4c9f-b0a1-cc1c1e156623/OceanDNA-b30427.fa --refList OceanDNA-b30427/target_genomes.txt --output OceanDNA-b30427/fastani_result.tsv --threads 1
[2023-03-18 20:14:12,406] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:12,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c53e468-a120-4832-9284-022c84abb904/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:12,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c53e468-a120-4832-9284-022c84abb904/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:12,419] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:12,419] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:14:12,419] [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 pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	80.7718	506	1115	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	80.4392	457	1115	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	78.888	419	1115	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.6187	263	1115	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.5905	269	1115	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.5884	259	1115	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.4909	249	1115	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.4818	258	1115	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	77.4494	213	1115	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.4343	253	1115	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.43	260	1115	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.3009	278	1115	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.274	241	1115	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.0982	288	1115	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.8074	177	1115	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.7472	142	1115	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.7464	191	1115	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	76.4052	145	1115	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.3943	104	1115	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	76.0882	75	1115	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.0311	95	1115	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:14:12,419] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30427/tc_result.tsv
[2023-03-18 20:14:12,420] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:12,420] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:12,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c53e468-a120-4832-9284-022c84abb904/dqc_reference/checkm_data
[2023-03-18 20:14:12,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:12,425] [INFO] Task started: CheckM
[2023-03-18 20:14:12,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30427/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30427/checkm_input OceanDNA-b30427/checkm_result
[2023-03-18 20:15:06,265] [INFO] Task succeeded: CheckM
[2023-03-18 20:15:06,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:15:06,269] [INFO] ===== Completeness check finished =====
[2023-03-18 20:15:06,269] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:15:06,269] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30427/markers.fasta)
[2023-03-18 20:15:06,269] [INFO] Task started: Blastn
[2023-03-18 20:15:06,269] [INFO] Running command: blastn -query OceanDNA-b30427/markers.fasta -db /var/lib/cwl/stg3c53e468-a120-4832-9284-022c84abb904/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30427/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:15:07,508] [INFO] Task succeeded: Blastn
[2023-03-18 20:15:07,800] [INFO] Selected 12 target genomes.
[2023-03-18 20:15:07,800] [INFO] Target genome list was writen to OceanDNA-b30427/target_genomes_gtdb.txt
[2023-03-18 20:15:07,934] [INFO] Task started: fastANI
[2023-03-18 20:15:07,935] [INFO] Running command: fastANI --query /var/lib/cwl/stgef244568-12f4-4c9f-b0a1-cc1c1e156623/OceanDNA-b30427.fa --refList OceanDNA-b30427/target_genomes_gtdb.txt --output OceanDNA-b30427/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:15:16,934] [INFO] Task succeeded: fastANI
[2023-03-18 20:15:16,941] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:15:16,942] [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_002731875.1	s__Sulfitobacter sp002731875	99.9671	1098	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.91	99.88	0.91	0.87	3	conclusive
GCA_011050655.1	s__Sulfitobacter sp011050655	86.561	869	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	80.7842	505	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_900103185.1	s__Sulfitobacter litoralis	80.4525	456	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_006064855.1	s__Sulfitobacter sp006064855	79.9869	448	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	79.5835	504	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000156335.1	s__Sulfitobacter sp000156335	79.239	483	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	79.1508	379	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.5173	234	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.43	260	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_900143525.1	s__Ruegeria sp900143525	76.8211	133	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.674	174	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-18 20:15:16,942] [INFO] GTDB search result was written to OceanDNA-b30427/result_gtdb.tsv
[2023-03-18 20:15:16,942] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:15:16,944] [INFO] DFAST_QC result json was written to OceanDNA-b30427/dqc_result.json
[2023-03-18 20:15:16,944] [INFO] DFAST_QC completed!
[2023-03-18 20:15:16,944] [INFO] Total running time: 0h1m44s