[2024-01-24 12:47:05,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,554] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd9232db-b38e-4a44-adff-9708c5ff9e62/dqc_reference
[2024-01-24 12:47:06,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,743] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg91a7b004-9a62-4e62-b988-39e967385715/GCF_003428685.1_ASM342868v1_genomic.fna.gz | prodigal -d GCF_003428685.1_ASM342868v1_genomic.fna/cds.fna -a GCF_003428685.1_ASM342868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:18,203] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:18,203] [INFO] Task started: HMMsearch
[2024-01-24 12:47:18,203] [INFO] Running command: hmmsearch --tblout GCF_003428685.1_ASM342868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd9232db-b38e-4a44-adff-9708c5ff9e62/dqc_reference/reference_markers.hmm GCF_003428685.1_ASM342868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:18,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:18,457] [INFO] Found 6/6 markers.
[2024-01-24 12:47:18,494] [INFO] Query marker FASTA was written to GCF_003428685.1_ASM342868v1_genomic.fna/markers.fasta
[2024-01-24 12:47:18,495] [INFO] Task started: Blastn
[2024-01-24 12:47:18,495] [INFO] Running command: blastn -query GCF_003428685.1_ASM342868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd9232db-b38e-4a44-adff-9708c5ff9e62/dqc_reference/reference_markers.fasta -out GCF_003428685.1_ASM342868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:19,306] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:19,309] [INFO] Selected 17 target genomes.
[2024-01-24 12:47:19,309] [INFO] Target genome list was writen to GCF_003428685.1_ASM342868v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:19,316] [INFO] Task started: fastANI
[2024-01-24 12:47:19,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg91a7b004-9a62-4e62-b988-39e967385715/GCF_003428685.1_ASM342868v1_genomic.fna.gz --refList GCF_003428685.1_ASM342868v1_genomic.fna/target_genomes.txt --output GCF_003428685.1_ASM342868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:31,675] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:31,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd9232db-b38e-4a44-adff-9708c5ff9e62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:31,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd9232db-b38e-4a44-adff-9708c5ff9e62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:31,690] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:31,691] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:31,691] [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
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	100.0	1274	1276	95	conclusive
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	99.9824	1274	1276	95	conclusive
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	77.6675	268	1276	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.356	225	1276	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.3115	243	1276	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	77.2619	206	1276	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.2312	207	1276	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	77.0793	209	1276	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.0068	151	1276	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	76.573	99	1276	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.5382	111	1276	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.4419	96	1276	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.4336	125	1276	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.4213	122	1276	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.3679	105	1276	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	76.2567	50	1276	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.0893	103	1276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:31,692] [INFO] DFAST Taxonomy check result was written to GCF_003428685.1_ASM342868v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:31,694] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:31,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:31,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd9232db-b38e-4a44-adff-9708c5ff9e62/dqc_reference/checkm_data
[2024-01-24 12:47:31,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:31,735] [INFO] Task started: CheckM
[2024-01-24 12:47:31,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003428685.1_ASM342868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003428685.1_ASM342868v1_genomic.fna/checkm_input GCF_003428685.1_ASM342868v1_genomic.fna/checkm_result
[2024-01-24 12:48:07,417] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:07,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:07,445] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:07,446] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:07,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003428685.1_ASM342868v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:07,446] [INFO] Task started: Blastn
[2024-01-24 12:48:07,446] [INFO] Running command: blastn -query GCF_003428685.1_ASM342868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd9232db-b38e-4a44-adff-9708c5ff9e62/dqc_reference/reference_markers_gtdb.fasta -out GCF_003428685.1_ASM342868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:08,805] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:08,809] [INFO] Selected 20 target genomes.
[2024-01-24 12:48:08,809] [INFO] Target genome list was writen to GCF_003428685.1_ASM342868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:08,826] [INFO] Task started: fastANI
[2024-01-24 12:48:08,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg91a7b004-9a62-4e62-b988-39e967385715/GCF_003428685.1_ASM342868v1_genomic.fna.gz --refList GCF_003428685.1_ASM342868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003428685.1_ASM342868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:21,745] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:21,761] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:21,761] [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
GCF_004340525.1	s__Chromatocurvus halotolerans	99.9824	1274	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_000764025.1	s__Pseudohaliea rubra	77.6675	268	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Pseudohaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.5136	268	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	77.356	225	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	77.3515	231	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_003402235.1	s__Parahaliea mediterranea	77.2994	244	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	77.2619	206	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_003457605.1	s__Halioglobus sediminis	77.2312	207	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_002699145.1	s__Halioglobus sp002699145	77.2106	210	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_009937575.1	s__Halioglobus sp009937575	77.0492	174	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_002692965.1	s__NZNC01 sp002692965	77.0452	229	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCA_004354085.1	s__Halioglobus sp004354085	77.0244	150	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_008370495.1	s__Halioglobus sp008370495	76.6736	164	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_002416125.1	s__Haliea sp002416125	76.6004	210	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_009388985.1	s__Halioglobus maricola	76.573	99	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_900115715.1	s__Pseudomonas_K sagittaria	76.4228	117	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	76.4213	122	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	76.3001	106	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646405.1	s__Halioglobus sp003646405	76.2155	84	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:21,762] [INFO] GTDB search result was written to GCF_003428685.1_ASM342868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:21,764] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:21,768] [INFO] DFAST_QC result json was written to GCF_003428685.1_ASM342868v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:21,768] [INFO] DFAST_QC completed!
[2024-01-24 12:48:21,768] [INFO] Total running time: 0h1m16s