[2023-03-15 13:20:53,600] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:53,600] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:53,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg30b71a16-cc32-4b82-b3c7-8d047e6c4843/dqc_reference
[2023-03-15 13:20:54,792] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:54,793] [INFO] Task started: Prodigal
[2023-03-15 13:20:54,793] [INFO] Running command: cat /var/lib/cwl/stg86cead91-a9f0-4224-a021-8b18dce11529/OceanDNA-b29583.fa | prodigal -d OceanDNA-b29583/cds.fna -a OceanDNA-b29583/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:10,215] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:10,215] [INFO] Task started: HMMsearch
[2023-03-15 13:21:10,215] [INFO] Running command: hmmsearch --tblout OceanDNA-b29583/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30b71a16-cc32-4b82-b3c7-8d047e6c4843/dqc_reference/reference_markers.hmm OceanDNA-b29583/protein.faa > /dev/null
[2023-03-15 13:21:10,536] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:10,536] [INFO] Found 6/6 markers.
[2023-03-15 13:21:10,554] [INFO] Query marker FASTA was written to OceanDNA-b29583/markers.fasta
[2023-03-15 13:21:10,556] [INFO] Task started: Blastn
[2023-03-15 13:21:10,556] [INFO] Running command: blastn -query OceanDNA-b29583/markers.fasta -db /var/lib/cwl/stg30b71a16-cc32-4b82-b3c7-8d047e6c4843/dqc_reference/reference_markers.fasta -out OceanDNA-b29583/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:11,349] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:11,351] [INFO] Selected 14 target genomes.
[2023-03-15 13:21:11,351] [INFO] Target genome list was writen to OceanDNA-b29583/target_genomes.txt
[2023-03-15 13:21:11,363] [INFO] Task started: fastANI
[2023-03-15 13:21:11,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg86cead91-a9f0-4224-a021-8b18dce11529/OceanDNA-b29583.fa --refList OceanDNA-b29583/target_genomes.txt --output OceanDNA-b29583/fastani_result.tsv --threads 1
[2023-03-15 13:21:20,492] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:20,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30b71a16-cc32-4b82-b3c7-8d047e6c4843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:20,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30b71a16-cc32-4b82-b3c7-8d047e6c4843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:20,506] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:20,506] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:21:20,506] [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
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	78.9618	361	775	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	78.9296	365	775	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	78.8412	340	775	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	78.7015	384	775	95	below_threshold
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	78.4914	391	775	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.3255	228	775	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	76.7696	137	775	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.3368	79	775	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	76.1662	83	775	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.1312	67	775	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.073	79	775	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.0423	92	775	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	75.882	65	775	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.6566	70	775	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:20,507] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29583/tc_result.tsv
[2023-03-15 13:21:20,507] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:20,508] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:20,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30b71a16-cc32-4b82-b3c7-8d047e6c4843/dqc_reference/checkm_data
[2023-03-15 13:21:20,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:20,513] [INFO] Task started: CheckM
[2023-03-15 13:21:20,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29583/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29583/checkm_input OceanDNA-b29583/checkm_result
[2023-03-15 13:22:03,129] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:03,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:03,134] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:03,134] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:03,134] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29583/markers.fasta)
[2023-03-15 13:22:03,134] [INFO] Task started: Blastn
[2023-03-15 13:22:03,134] [INFO] Running command: blastn -query OceanDNA-b29583/markers.fasta -db /var/lib/cwl/stg30b71a16-cc32-4b82-b3c7-8d047e6c4843/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29583/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:04,414] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:04,416] [INFO] Selected 9 target genomes.
[2023-03-15 13:22:04,416] [INFO] Target genome list was writen to OceanDNA-b29583/target_genomes_gtdb.txt
[2023-03-15 13:22:04,423] [INFO] Task started: fastANI
[2023-03-15 13:22:04,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg86cead91-a9f0-4224-a021-8b18dce11529/OceanDNA-b29583.fa --refList OceanDNA-b29583/target_genomes_gtdb.txt --output OceanDNA-b29583/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:10,281] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:10,286] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:22:10,287] [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_018608045.1	s__Octadecabacter sp018608045	99.1663	657	775	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	conclusive
GCA_018500005.1	s__Octadecabacter sp018500005	78.9872	277	775	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187845.1	s__Octadecabacter temperatus	78.9618	361	775	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900185015.1	s__Octadecabacter ascidiaceicola	78.8412	340	775	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017886375.1	s__Octadecabacter sp017886375	78.7552	371	775	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000155735.2	s__Octadecabacter arcticus	78.7229	382	775	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
GCF_000155675.2	s__Octadecabacter antarcticus	78.4815	392	775	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861045.1	s__Octadecabacter sp018861045	78.3523	339	775	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	77.3255	228	775	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:10,287] [INFO] GTDB search result was written to OceanDNA-b29583/result_gtdb.tsv
[2023-03-15 13:22:10,287] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:10,289] [INFO] DFAST_QC result json was written to OceanDNA-b29583/dqc_result.json
[2023-03-15 13:22:10,289] [INFO] DFAST_QC completed!
[2023-03-15 13:22:10,290] [INFO] Total running time: 0h1m17s