[2023-03-15 21:16:33,624] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:16:33,624] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:16:33,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg13f3b173-288c-43e9-86e8-823b5a80f7b7/dqc_reference
[2023-03-15 21:16:35,481] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:16:35,482] [INFO] Task started: Prodigal
[2023-03-15 21:16:35,482] [INFO] Running command: cat /var/lib/cwl/stg559f17d5-4333-4811-b8bd-df4239639932/OceanDNA-b38180.fa | prodigal -d OceanDNA-b38180/cds.fna -a OceanDNA-b38180/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:16:59,490] [INFO] Task succeeded: Prodigal
[2023-03-15 21:16:59,490] [INFO] Task started: HMMsearch
[2023-03-15 21:16:59,490] [INFO] Running command: hmmsearch --tblout OceanDNA-b38180/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13f3b173-288c-43e9-86e8-823b5a80f7b7/dqc_reference/reference_markers.hmm OceanDNA-b38180/protein.faa > /dev/null
[2023-03-15 21:16:59,707] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:16:59,707] [INFO] Found 6/6 markers.
[2023-03-15 21:16:59,730] [INFO] Query marker FASTA was written to OceanDNA-b38180/markers.fasta
[2023-03-15 21:16:59,732] [INFO] Task started: Blastn
[2023-03-15 21:16:59,732] [INFO] Running command: blastn -query OceanDNA-b38180/markers.fasta -db /var/lib/cwl/stg13f3b173-288c-43e9-86e8-823b5a80f7b7/dqc_reference/reference_markers.fasta -out OceanDNA-b38180/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:17:00,470] [INFO] Task succeeded: Blastn
[2023-03-15 21:17:00,470] [INFO] Selected 14 target genomes.
[2023-03-15 21:17:00,471] [INFO] Target genome list was writen to OceanDNA-b38180/target_genomes.txt
[2023-03-15 21:17:00,480] [INFO] Task started: fastANI
[2023-03-15 21:17:00,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg559f17d5-4333-4811-b8bd-df4239639932/OceanDNA-b38180.fa --refList OceanDNA-b38180/target_genomes.txt --output OceanDNA-b38180/fastani_result.tsv --threads 1
[2023-03-15 21:17:10,644] [INFO] Task succeeded: fastANI
[2023-03-15 21:17:10,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13f3b173-288c-43e9-86e8-823b5a80f7b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:17:10,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13f3b173-288c-43e9-86e8-823b5a80f7b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:17:10,653] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:17:10,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:17:10,654] [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
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	79.2236	450	1276	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	79.2158	500	1276	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	79.0373	403	1276	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	78.7514	447	1276	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	78.6752	379	1276	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	78.5601	427	1276	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	78.2996	379	1276	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.6049	276	1276	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	77.4657	303	1276	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	77.0641	171	1276	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.0299	149	1276	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	76.9509	140	1276	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.745	188	1276	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	76.5773	174	1276	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:17:10,654] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38180/tc_result.tsv
[2023-03-15 21:17:10,654] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:17:10,654] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:17:10,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13f3b173-288c-43e9-86e8-823b5a80f7b7/dqc_reference/checkm_data
[2023-03-15 21:17:10,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:17:10,685] [INFO] Task started: CheckM
[2023-03-15 21:17:10,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38180/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38180/checkm_input OceanDNA-b38180/checkm_result
[2023-03-15 21:18:10,959] [INFO] Task succeeded: CheckM
[2023-03-15 21:18:10,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:18:10,962] [INFO] ===== Completeness check finished =====
[2023-03-15 21:18:10,962] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:18:10,962] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38180/markers.fasta)
[2023-03-15 21:18:10,963] [INFO] Task started: Blastn
[2023-03-15 21:18:10,963] [INFO] Running command: blastn -query OceanDNA-b38180/markers.fasta -db /var/lib/cwl/stg13f3b173-288c-43e9-86e8-823b5a80f7b7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38180/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:18:12,230] [INFO] Task succeeded: Blastn
[2023-03-15 21:18:12,231] [INFO] Selected 16 target genomes.
[2023-03-15 21:18:12,231] [INFO] Target genome list was writen to OceanDNA-b38180/target_genomes_gtdb.txt
[2023-03-15 21:18:12,500] [INFO] Task started: fastANI
[2023-03-15 21:18:12,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg559f17d5-4333-4811-b8bd-df4239639932/OceanDNA-b38180.fa --refList OceanDNA-b38180/target_genomes_gtdb.txt --output OceanDNA-b38180/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:18:25,606] [INFO] Task succeeded: fastANI
[2023-03-15 21:18:25,616] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:18:25,616] [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_002692965.1	s__NZNC01 sp002692965	99.9707	1238	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	conclusive
GCF_017255185.1	s__Parahaliea mediterranea_A	79.6206	504	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	79.2325	450	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	79.2217	499	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423125.1	s__Haliea salexigens	79.0524	403	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCA_002414665.1	s__Haliea sp002414665	78.8956	402	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCA_002699145.1	s__Halioglobus sp002699145	78.8233	382	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_008064665.1	s__Parahaliea maris	78.7617	446	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	78.7557	381	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669285.1	s__Kineobactrum salinum	78.6752	379	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719295.1	s__Haliea alexandrii	78.5601	427	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002416125.1	s__Haliea sp002416125	78.3566	426	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCF_003457605.1	s__Halioglobus sediminis	78.2999	379	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	77.9575	282	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	77.605	276	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002868715.1	s__Kineobactrum sediminis	77.4657	303	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:18:25,616] [INFO] GTDB search result was written to OceanDNA-b38180/result_gtdb.tsv
[2023-03-15 21:18:25,616] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:18:25,618] [INFO] DFAST_QC result json was written to OceanDNA-b38180/dqc_result.json
[2023-03-15 21:18:25,618] [INFO] DFAST_QC completed!
[2023-03-15 21:18:25,618] [INFO] Total running time: 0h1m52s