[2023-03-18 00:35:04,585] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:04,590] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:04,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f2ff434-a8ff-4622-b2c3-cbb3c6a96467/dqc_reference
[2023-03-18 00:35:05,658] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:05,658] [INFO] Task started: Prodigal
[2023-03-18 00:35:05,658] [INFO] Running command: cat /var/lib/cwl/stgf3c79de6-e613-49ea-b82e-d398743c8b24/OceanDNA-b37582.fa | prodigal -d OceanDNA-b37582/cds.fna -a OceanDNA-b37582/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:27,156] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:27,156] [INFO] Task started: HMMsearch
[2023-03-18 00:35:27,157] [INFO] Running command: hmmsearch --tblout OceanDNA-b37582/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f2ff434-a8ff-4622-b2c3-cbb3c6a96467/dqc_reference/reference_markers.hmm OceanDNA-b37582/protein.faa > /dev/null
[2023-03-18 00:35:27,417] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:27,418] [INFO] Found 6/6 markers.
[2023-03-18 00:35:27,439] [INFO] Query marker FASTA was written to OceanDNA-b37582/markers.fasta
[2023-03-18 00:35:27,439] [INFO] Task started: Blastn
[2023-03-18 00:35:27,439] [INFO] Running command: blastn -query OceanDNA-b37582/markers.fasta -db /var/lib/cwl/stg7f2ff434-a8ff-4622-b2c3-cbb3c6a96467/dqc_reference/reference_markers.fasta -out OceanDNA-b37582/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:28,238] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:28,239] [INFO] Selected 18 target genomes.
[2023-03-18 00:35:28,239] [INFO] Target genome list was writen to OceanDNA-b37582/target_genomes.txt
[2023-03-18 00:35:28,246] [INFO] Task started: fastANI
[2023-03-18 00:35:28,246] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3c79de6-e613-49ea-b82e-d398743c8b24/OceanDNA-b37582.fa --refList OceanDNA-b37582/target_genomes.txt --output OceanDNA-b37582/fastani_result.tsv --threads 1
[2023-03-18 00:35:41,639] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:41,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f2ff434-a8ff-4622-b2c3-cbb3c6a96467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:41,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f2ff434-a8ff-4622-b2c3-cbb3c6a96467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:41,649] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:41,649] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:35:41,649] [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
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	81.3608	804	1115	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	81.2579	816	1115	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	78.0932	308	1115	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.0413	348	1115	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.9408	343	1115	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.4891	316	1115	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	77.36	299	1115	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.2037	276	1115	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.7571	155	1115	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.7314	153	1115	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.6502	183	1115	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	76.6412	187	1115	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	76.5243	194	1115	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.2879	93	1115	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	76.0744	78	1115	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	75.435	58	1115	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:35:41,649] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37582/tc_result.tsv
[2023-03-18 00:35:41,649] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:41,649] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:41,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f2ff434-a8ff-4622-b2c3-cbb3c6a96467/dqc_reference/checkm_data
[2023-03-18 00:35:41,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:41,654] [INFO] Task started: CheckM
[2023-03-18 00:35:41,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37582/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37582/checkm_input OceanDNA-b37582/checkm_result
[2023-03-18 00:36:35,209] [INFO] Task succeeded: CheckM
[2023-03-18 00:36:35,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:36:35,212] [INFO] ===== Completeness check finished =====
[2023-03-18 00:36:35,212] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:36:35,212] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37582/markers.fasta)
[2023-03-18 00:36:35,212] [INFO] Task started: Blastn
[2023-03-18 00:36:35,213] [INFO] Running command: blastn -query OceanDNA-b37582/markers.fasta -db /var/lib/cwl/stg7f2ff434-a8ff-4622-b2c3-cbb3c6a96467/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37582/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:36:36,588] [INFO] Task succeeded: Blastn
[2023-03-18 00:36:36,588] [INFO] Selected 10 target genomes.
[2023-03-18 00:36:36,589] [INFO] Target genome list was writen to OceanDNA-b37582/target_genomes_gtdb.txt
[2023-03-18 00:36:36,598] [INFO] Task started: fastANI
[2023-03-18 00:36:36,598] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3c79de6-e613-49ea-b82e-d398743c8b24/OceanDNA-b37582.fa --refList OceanDNA-b37582/target_genomes_gtdb.txt --output OceanDNA-b37582/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:36:44,613] [INFO] Task succeeded: fastANI
[2023-03-18 00:36:44,619] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:36:44,619] [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_002416125.1	s__Haliea sp002416125	99.1426	1077	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	conclusive
GCA_002414665.1	s__Haliea sp002414665	90.3635	984	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCF_000423125.1	s__Haliea salexigens	81.3608	804	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_003719295.1	s__Haliea alexandrii	81.2549	817	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	78.1397	387	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_010669285.1	s__Kineobactrum salinum	78.0812	309	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	78.0411	348	1115	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	77.9502	342	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	77.4329	278	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_004340525.1	s__Chromatocurvus halotolerans	76.6502	183	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:36:44,619] [INFO] GTDB search result was written to OceanDNA-b37582/result_gtdb.tsv
[2023-03-18 00:36:44,620] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:36:44,621] [INFO] DFAST_QC result json was written to OceanDNA-b37582/dqc_result.json
[2023-03-18 00:36:44,621] [INFO] DFAST_QC completed!
[2023-03-18 00:36:44,621] [INFO] Total running time: 0h1m40s