[2023-03-18 07:29:30,336] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,337] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,337] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb5ea48a-6237-40ae-aa27-713103249145/dqc_reference
[2023-03-18 07:29:31,935] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,936] [INFO] Running command: cat /var/lib/cwl/stg509a4400-3b90-4261-b4c4-a6c6c7ae8b59/OceanDNA-b28039.fa | prodigal -d OceanDNA-b28039/cds.fna -a OceanDNA-b28039/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:45,808] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:45,808] [INFO] Task started: HMMsearch
[2023-03-18 07:29:45,808] [INFO] Running command: hmmsearch --tblout OceanDNA-b28039/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb5ea48a-6237-40ae-aa27-713103249145/dqc_reference/reference_markers.hmm OceanDNA-b28039/protein.faa > /dev/null
[2023-03-18 07:29:45,982] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:45,982] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg509a4400-3b90-4261-b4c4-a6c6c7ae8b59/OceanDNA-b28039.fa]
[2023-03-18 07:29:45,999] [INFO] Query marker FASTA was written to OceanDNA-b28039/markers.fasta
[2023-03-18 07:29:46,000] [INFO] Task started: Blastn
[2023-03-18 07:29:46,000] [INFO] Running command: blastn -query OceanDNA-b28039/markers.fasta -db /var/lib/cwl/stgcb5ea48a-6237-40ae-aa27-713103249145/dqc_reference/reference_markers.fasta -out OceanDNA-b28039/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:46,582] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:46,583] [INFO] Selected 22 target genomes.
[2023-03-18 07:29:46,583] [INFO] Target genome list was writen to OceanDNA-b28039/target_genomes.txt
[2023-03-18 07:29:46,594] [INFO] Task started: fastANI
[2023-03-18 07:29:46,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg509a4400-3b90-4261-b4c4-a6c6c7ae8b59/OceanDNA-b28039.fa --refList OceanDNA-b28039/target_genomes.txt --output OceanDNA-b28039/fastani_result.tsv --threads 1
[2023-03-18 07:29:59,590] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:59,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb5ea48a-6237-40ae-aa27-713103249145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:59,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb5ea48a-6237-40ae-aa27-713103249145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:59,601] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:59,601] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:29:59,602] [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
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	77.4594	164	724	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	76.9566	78	724	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	76.8717	105	724	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	76.7919	120	724	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	76.7278	117	724	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.7248	106	724	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	76.6975	115	724	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.6179	96	724	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	76.5693	74	724	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	76.5613	85	724	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.5566	99	724	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	76.4633	75	724	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.4044	89	724	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.3972	88	724	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	76.2228	73	724	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.1994	74	724	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	76.1954	72	724	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	75.9991	57	724	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:29:59,602] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28039/tc_result.tsv
[2023-03-18 07:29:59,602] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:59,602] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:59,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb5ea48a-6237-40ae-aa27-713103249145/dqc_reference/checkm_data
[2023-03-18 07:29:59,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:59,608] [INFO] Task started: CheckM
[2023-03-18 07:29:59,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28039/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28039/checkm_input OceanDNA-b28039/checkm_result
[2023-03-18 07:30:37,825] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:37,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:37,828] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:37,828] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:37,828] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28039/markers.fasta)
[2023-03-18 07:30:37,828] [INFO] Task started: Blastn
[2023-03-18 07:30:37,828] [INFO] Running command: blastn -query OceanDNA-b28039/markers.fasta -db /var/lib/cwl/stgcb5ea48a-6237-40ae-aa27-713103249145/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28039/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:38,739] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:38,740] [INFO] Selected 12 target genomes.
[2023-03-18 07:30:38,740] [INFO] Target genome list was writen to OceanDNA-b28039/target_genomes_gtdb.txt
[2023-03-18 07:30:38,772] [INFO] Task started: fastANI
[2023-03-18 07:30:38,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg509a4400-3b90-4261-b4c4-a6c6c7ae8b59/OceanDNA-b28039.fa --refList OceanDNA-b28039/target_genomes_gtdb.txt --output OceanDNA-b28039/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:45,655] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:45,663] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:30:45,663] [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_905182105.1	s__Ascidiaceihabitans sp905182105	92.5382	606	724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478745.1	s__Ascidiaceihabitans sp002478745	90.9358	585	724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.75	99.75	0.89	0.89	2	-
GCA_018647275.1	s__Ascidiaceihabitans sp018647275	90.217	356	724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182355.1	s__Ascidiaceihabitans sp905182355	78.8984	327	724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	77.4758	163	724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	76.9385	104	724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	76.8717	105	724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_000622405.1	s__Sulfitobacter donghicola	76.7919	120	724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900116285.1	s__Sulfitobacter marinus	76.7248	106	724	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	76.6713	92	724	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	76.6017	86	724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346665.1	s__Sulfitobacter maritimus	76.1954	72	724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:45,664] [INFO] GTDB search result was written to OceanDNA-b28039/result_gtdb.tsv
[2023-03-18 07:30:45,664] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:45,665] [INFO] DFAST_QC result json was written to OceanDNA-b28039/dqc_result.json
[2023-03-18 07:30:45,666] [INFO] DFAST_QC completed!
[2023-03-18 07:30:45,666] [INFO] Total running time: 0h1m15s