[2023-03-15 22:44:22,200] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:44:22,216] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:44:22,216] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a2fd168-a466-4953-b179-7d0ef9dca04e/dqc_reference
[2023-03-15 22:44:23,325] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:44:23,325] [INFO] Task started: Prodigal
[2023-03-15 22:44:23,325] [INFO] Running command: cat /var/lib/cwl/stgfc55c91c-9feb-4503-88f5-58a02a6cdf0e/OceanDNA-b30234.fa | prodigal -d OceanDNA-b30234/cds.fna -a OceanDNA-b30234/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:44:46,527] [INFO] Task succeeded: Prodigal
[2023-03-15 22:44:46,527] [INFO] Task started: HMMsearch
[2023-03-15 22:44:46,527] [INFO] Running command: hmmsearch --tblout OceanDNA-b30234/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a2fd168-a466-4953-b179-7d0ef9dca04e/dqc_reference/reference_markers.hmm OceanDNA-b30234/protein.faa > /dev/null
[2023-03-15 22:44:46,749] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:44:46,749] [INFO] Found 6/6 markers.
[2023-03-15 22:44:46,875] [INFO] Query marker FASTA was written to OceanDNA-b30234/markers.fasta
[2023-03-15 22:44:46,876] [INFO] Task started: Blastn
[2023-03-15 22:44:46,876] [INFO] Running command: blastn -query OceanDNA-b30234/markers.fasta -db /var/lib/cwl/stg6a2fd168-a466-4953-b179-7d0ef9dca04e/dqc_reference/reference_markers.fasta -out OceanDNA-b30234/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:47,628] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:47,678] [INFO] Selected 24 target genomes.
[2023-03-15 22:44:47,679] [INFO] Target genome list was writen to OceanDNA-b30234/target_genomes.txt
[2023-03-15 22:44:47,690] [INFO] Task started: fastANI
[2023-03-15 22:44:47,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc55c91c-9feb-4503-88f5-58a02a6cdf0e/OceanDNA-b30234.fa --refList OceanDNA-b30234/target_genomes.txt --output OceanDNA-b30234/fastani_result.tsv --threads 1
[2023-03-15 22:45:04,849] [INFO] Task succeeded: fastANI
[2023-03-15 22:45:04,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a2fd168-a466-4953-b179-7d0ef9dca04e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:45:04,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a2fd168-a466-4953-b179-7d0ef9dca04e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:45:04,864] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:45:04,864] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:45:04,864] [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 mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.4286	509	1185	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.2789	439	1185	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.2611	433	1185	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	78.047	469	1185	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	78.0193	476	1185	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	78.0001	454	1185	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	77.9087	441	1185	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.8386	389	1185	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	77.8265	349	1185	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.8123	429	1185	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.6385	365	1185	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	77.6237	337	1185	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.6003	359	1185	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.5759	378	1185	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.4756	399	1185	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	77.4677	344	1185	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.025	251	1185	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.679	259	1185	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	76.6623	160	1185	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.4443	162	1185	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.4197	208	1185	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.3276	173	1185	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.2483	104	1185	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	76.0883	128	1185	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:45:04,867] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30234/tc_result.tsv
[2023-03-15 22:45:04,872] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:45:04,872] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:45:04,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a2fd168-a466-4953-b179-7d0ef9dca04e/dqc_reference/checkm_data
[2023-03-15 22:45:04,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:45:04,919] [INFO] Task started: CheckM
[2023-03-15 22:45:04,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30234/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30234/checkm_input OceanDNA-b30234/checkm_result
[2023-03-15 22:46:08,064] [INFO] Task succeeded: CheckM
[2023-03-15 22:46:08,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:46:08,385] [INFO] ===== Completeness check finished =====
[2023-03-15 22:46:08,385] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:46:08,385] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30234/markers.fasta)
[2023-03-15 22:46:08,386] [INFO] Task started: Blastn
[2023-03-15 22:46:08,386] [INFO] Running command: blastn -query OceanDNA-b30234/markers.fasta -db /var/lib/cwl/stg6a2fd168-a466-4953-b179-7d0ef9dca04e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30234/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:46:09,756] [INFO] Task succeeded: Blastn
[2023-03-15 22:46:09,774] [INFO] Selected 18 target genomes.
[2023-03-15 22:46:09,774] [INFO] Target genome list was writen to OceanDNA-b30234/target_genomes_gtdb.txt
[2023-03-15 22:46:09,879] [INFO] Task started: fastANI
[2023-03-15 22:46:09,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc55c91c-9feb-4503-88f5-58a02a6cdf0e/OceanDNA-b30234.fa --refList OceanDNA-b30234/target_genomes_gtdb.txt --output OceanDNA-b30234/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:46:24,043] [INFO] Task succeeded: fastANI
[2023-03-15 22:46:24,053] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:46:24,054] [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
GCF_003335585.1	s__Sulfitobacter sp003335585	80.156	761	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	80.0544	702	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	79.3189	641	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	78.6926	564	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	78.4438	507	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	78.3275	489	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.2789	439	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003352065.1	s__Sulfitobacter sp003352065	78.2738	417	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.0966	418	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622365.1	s__Sulfitobacter noctilucae	78.0001	454	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156335.1	s__Sulfitobacter sp000156335	77.9826	414	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	77.9087	441	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.8123	429	1185	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_017743885.1	s__Sulfitobacter sp001635605	77.7458	410	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCA_013139555.1	s__Sulfitobacter sp013139555	77.7419	314	1185	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	77.6935	391	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_014763045.1	s__Sulfitobacter aestuariivivens	77.4835	398	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002405.1	s__Sulfitobacter sp013002405	77.3194	320	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:46:24,057] [INFO] GTDB search result was written to OceanDNA-b30234/result_gtdb.tsv
[2023-03-15 22:46:24,059] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:46:24,068] [INFO] DFAST_QC result json was written to OceanDNA-b30234/dqc_result.json
[2023-03-15 22:46:24,068] [INFO] DFAST_QC completed!
[2023-03-15 22:46:24,069] [INFO] Total running time: 0h2m2s