[2023-03-14 10:56:00,387] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:56:00,387] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:56:00,387] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0e127c6-a3b6-4497-b3b8-784a2b0e0c43/dqc_reference
[2023-03-14 10:56:01,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:01,560] [INFO] Task started: Prodigal
[2023-03-14 10:56:01,560] [INFO] Running command: cat /var/lib/cwl/stg875cc927-95ca-4fbc-9bb7-d6bd351588dc/OceanDNA-b32883.fa | prodigal -d OceanDNA-b32883/cds.fna -a OceanDNA-b32883/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:13,330] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:13,330] [INFO] Task started: HMMsearch
[2023-03-14 10:56:13,330] [INFO] Running command: hmmsearch --tblout OceanDNA-b32883/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0e127c6-a3b6-4497-b3b8-784a2b0e0c43/dqc_reference/reference_markers.hmm OceanDNA-b32883/protein.faa > /dev/null
[2023-03-14 10:56:13,567] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:13,568] [INFO] Found 6/6 markers.
[2023-03-14 10:56:13,592] [INFO] Query marker FASTA was written to OceanDNA-b32883/markers.fasta
[2023-03-14 10:56:13,592] [INFO] Task started: Blastn
[2023-03-14 10:56:13,593] [INFO] Running command: blastn -query OceanDNA-b32883/markers.fasta -db /var/lib/cwl/stgf0e127c6-a3b6-4497-b3b8-784a2b0e0c43/dqc_reference/reference_markers.fasta -out OceanDNA-b32883/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:14,386] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:14,387] [INFO] Selected 34 target genomes.
[2023-03-14 10:56:14,387] [INFO] Target genome list was writen to OceanDNA-b32883/target_genomes.txt
[2023-03-14 10:56:14,408] [INFO] Task started: fastANI
[2023-03-14 10:56:14,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg875cc927-95ca-4fbc-9bb7-d6bd351588dc/OceanDNA-b32883.fa --refList OceanDNA-b32883/target_genomes.txt --output OceanDNA-b32883/fastani_result.tsv --threads 1
[2023-03-14 10:56:47,183] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:47,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0e127c6-a3b6-4497-b3b8-784a2b0e0c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:47,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0e127c6-a3b6-4497-b3b8-784a2b0e0c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:47,198] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:47,198] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:47,198] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.4185	94	621	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.2941	89	621	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.2735	80	621	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.2567	91	621	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.1096	65	621	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	76.0425	60	621	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.0089	64	621	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.0007	101	621	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.9583	60	621	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	75.8577	60	621	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	75.8081	59	621	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	75.8074	59	621	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	75.8074	59	621	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	75.7716	88	621	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.7604	85	621	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	75.7391	89	621	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	75.7009	66	621	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.6644	64	621	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	75.6161	62	621	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.6156	51	621	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.5735	57	621	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	75.5478	66	621	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	75.5145	61	621	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	75.4915	60	621	95	below_threshold
Methylobacterium brachiatum	strain=B0021	GCA_020523825.1	269660	269660	type	True	75.4124	58	621	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	75.3583	59	621	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:47,198] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32883/tc_result.tsv
[2023-03-14 10:56:47,199] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:47,199] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:47,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0e127c6-a3b6-4497-b3b8-784a2b0e0c43/dqc_reference/checkm_data
[2023-03-14 10:56:47,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:47,205] [INFO] Task started: CheckM
[2023-03-14 10:56:47,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32883/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32883/checkm_input OceanDNA-b32883/checkm_result
[2023-03-14 10:57:19,134] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:19,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:19,136] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:19,136] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:19,136] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32883/markers.fasta)
[2023-03-14 10:57:19,136] [INFO] Task started: Blastn
[2023-03-14 10:57:19,136] [INFO] Running command: blastn -query OceanDNA-b32883/markers.fasta -db /var/lib/cwl/stgf0e127c6-a3b6-4497-b3b8-784a2b0e0c43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32883/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:20,425] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:20,425] [INFO] Selected 14 target genomes.
[2023-03-14 10:57:20,425] [INFO] Target genome list was writen to OceanDNA-b32883/target_genomes_gtdb.txt
[2023-03-14 10:57:20,439] [INFO] Task started: fastANI
[2023-03-14 10:57:20,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg875cc927-95ca-4fbc-9bb7-d6bd351588dc/OceanDNA-b32883.fa --refList OceanDNA-b32883/target_genomes_gtdb.txt --output OceanDNA-b32883/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:29,066] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:29,074] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:29,074] [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_002708995.1	s__UBA7985 sp002708995	95.5086	544	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	95.44	95.44	0.84	0.83	3	conclusive
GCA_002711265.1	s__UBA7985 sp002711265	93.9487	463	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.38	98.76	0.89	0.83	3	-
GCA_002690455.1	s__UBA7985 sp002690455	80.7693	278	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700865.1	s__UBA7985 sp002700865	78.1175	185	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.96	99.96	0.93	0.93	2	-
GCA_002705565.1	s__UBA7985 sp002705565	77.707	209	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.09	99.09	0.80	0.80	2	-
GCA_003250275.1	s__Alpha-05 sp003250275	76.0169	51	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829925.1	s__Roseomonas coralli	75.8577	60	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861165.1	s__BOKV01 sp016861165	75.6732	57	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__BOKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653355.1	s__Rhodoplanes elegans	75.5735	57	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCA_001510895.1	s__Mesorhizobium loti_A	75.5168	65	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952465.1	s__Mesorhizobium sp003952465	75.4346	56	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_003015025.1	s__Nitratireductor_D sp003015025	75.4136	55	621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:29,074] [INFO] GTDB search result was written to OceanDNA-b32883/result_gtdb.tsv
[2023-03-14 10:57:29,074] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:29,076] [INFO] DFAST_QC result json was written to OceanDNA-b32883/dqc_result.json
[2023-03-14 10:57:29,076] [INFO] DFAST_QC completed!
[2023-03-14 10:57:29,076] [INFO] Total running time: 0h1m29s