[2023-07-01 04:06:01,082] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:06:01,084] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:06:01,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg61ef8ada-1df5-49cb-962c-4c4ffc4fbf84/dqc_reference
[2023-07-01 04:06:03,961] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:06:03,962] [INFO] Task started: Prodigal
[2023-07-01 04:06:03,963] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c65363d-abc4-4c57-ab07-726229f2eb6e/GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna.gz | prodigal -d GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/cds.fna -a GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:06:12,619] [INFO] Task succeeded: Prodigal
[2023-07-01 04:06:12,619] [INFO] Task started: HMMsearch
[2023-07-01 04:06:12,620] [INFO] Running command: hmmsearch --tblout GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61ef8ada-1df5-49cb-962c-4c4ffc4fbf84/dqc_reference/reference_markers.hmm GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:06:12,890] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:06:12,892] [INFO] Found 6/6 markers.
[2023-07-01 04:06:12,920] [INFO] Query marker FASTA was written to GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/markers.fasta
[2023-07-01 04:06:12,921] [INFO] Task started: Blastn
[2023-07-01 04:06:12,921] [INFO] Running command: blastn -query GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/markers.fasta -db /var/lib/cwl/stg61ef8ada-1df5-49cb-962c-4c4ffc4fbf84/dqc_reference/reference_markers.fasta -out GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:06:13,657] [INFO] Task succeeded: Blastn
[2023-07-01 04:06:13,662] [INFO] Selected 27 target genomes.
[2023-07-01 04:06:13,662] [INFO] Target genome list was writen to GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/target_genomes.txt
[2023-07-01 04:06:13,665] [INFO] Task started: fastANI
[2023-07-01 04:06:13,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c65363d-abc4-4c57-ab07-726229f2eb6e/GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna.gz --refList GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/target_genomes.txt --output GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:06:30,484] [INFO] Task succeeded: fastANI
[2023-07-01 04:06:30,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61ef8ada-1df5-49cb-962c-4c4ffc4fbf84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:06:30,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61ef8ada-1df5-49cb-962c-4c4ffc4fbf84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:06:30,513] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:06:30,514] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 04:06:30,514] [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
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	84.7924	525	671	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	79.3085	229	671	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	78.8605	236	671	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.4037	232	671	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	77.7723	194	671	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	77.5056	170	671	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	77.4695	176	671	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	77.4652	160	671	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	77.4376	160	671	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.4299	180	671	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	77.4054	182	671	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	77.3864	161	671	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	77.2411	154	671	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	77.1603	158	671	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	77.1532	136	671	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	76.9095	78	671	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	76.8141	144	671	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	76.7701	97	671	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	76.7645	130	671	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	76.752	92	671	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	76.7455	98	671	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	76.5932	111	671	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	76.5544	86	671	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	76.4142	100	671	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 04:06:30,517] [INFO] DFAST Taxonomy check result was written to GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/tc_result.tsv
[2023-07-01 04:06:30,518] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:06:30,519] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:06:30,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61ef8ada-1df5-49cb-962c-4c4ffc4fbf84/dqc_reference/checkm_data
[2023-07-01 04:06:30,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:06:30,552] [INFO] Task started: CheckM
[2023-07-01 04:06:30,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/checkm_input GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/checkm_result
[2023-07-01 04:07:01,882] [INFO] Task succeeded: CheckM
[2023-07-01 04:07:01,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 14.58%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-07-01 04:07:01,908] [INFO] ===== Completeness check finished =====
[2023-07-01 04:07:01,908] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:07:01,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/markers.fasta)
[2023-07-01 04:07:01,909] [INFO] Task started: Blastn
[2023-07-01 04:07:01,909] [INFO] Running command: blastn -query GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/markers.fasta -db /var/lib/cwl/stg61ef8ada-1df5-49cb-962c-4c4ffc4fbf84/dqc_reference/reference_markers_gtdb.fasta -out GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:07:03,246] [INFO] Task succeeded: Blastn
[2023-07-01 04:07:03,250] [INFO] Selected 12 target genomes.
[2023-07-01 04:07:03,250] [INFO] Target genome list was writen to GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:07:03,255] [INFO] Task started: fastANI
[2023-07-01 04:07:03,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c65363d-abc4-4c57-ab07-726229f2eb6e/GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna.gz --refList GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/target_genomes_gtdb.txt --output GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:07:10,443] [INFO] Task succeeded: fastANI
[2023-07-01 04:07:10,461] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:07:10,461] [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_903856995.1	s__Limnohabitans sp903856995	100.0	658	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003063475.1	s__Limnohabitans curvus	84.8078	524	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.49	98.49	0.87	0.87	2	-
GCF_003063545.1	s__Limnohabitans sp003063545	84.0496	502	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282445.1	s__Limnohabitans sp002282445	83.8109	472	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	100.00	100.00	0.99	0.99	3	-
GCA_903886485.1	s__Limnohabitans sp903886485	83.1802	473	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.98	99.98	0.98	0.98	3	-
GCA_903952885.1	s__Limnohabitans sp903952885	82.602	356	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.13	99.13	0.83	0.83	2	-
GCF_002778325.1	s__Limnohabitans sp002778325	82.0909	462	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000293865.2	s__Limnohabitans_A sp000293865	78.5179	212	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242005.1	s__Alicycliphilus sp018242005	76.7819	101	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217575.1	s__Xylophilus ampelinus	76.7706	98	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938955.1	s__Rhodoferax sp903938955	76.6977	72	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421705.1	s__Xylophilus sp001421705	76.5128	118	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 04:07:10,463] [INFO] GTDB search result was written to GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/result_gtdb.tsv
[2023-07-01 04:07:10,464] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:07:10,468] [INFO] DFAST_QC result json was written to GCA_903856995.1_freshwater_MAG_---_LJ-5-9m_bin-0025_genomic.fna/dqc_result.json
[2023-07-01 04:07:10,468] [INFO] DFAST_QC completed!
[2023-07-01 04:07:10,469] [INFO] Total running time: 0h1m9s