[2024-01-24 13:57:27,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:27,163] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:27,163] [INFO] DQC Reference Directory: /var/lib/cwl/stgd81468e0-b0a4-45bc-9563-df8b8ccb54f9/dqc_reference
[2024-01-24 13:57:28,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:28,426] [INFO] Task started: Prodigal
[2024-01-24 13:57:28,426] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5935a0f-4a33-4bd1-b497-c7001c3b452d/GCF_002310815.1_ASM231081v1_genomic.fna.gz | prodigal -d GCF_002310815.1_ASM231081v1_genomic.fna/cds.fna -a GCF_002310815.1_ASM231081v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:38,848] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:38,849] [INFO] Task started: HMMsearch
[2024-01-24 13:57:38,849] [INFO] Running command: hmmsearch --tblout GCF_002310815.1_ASM231081v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd81468e0-b0a4-45bc-9563-df8b8ccb54f9/dqc_reference/reference_markers.hmm GCF_002310815.1_ASM231081v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:39,178] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:39,179] [INFO] Found 6/6 markers.
[2024-01-24 13:57:39,219] [INFO] Query marker FASTA was written to GCF_002310815.1_ASM231081v1_genomic.fna/markers.fasta
[2024-01-24 13:57:39,220] [INFO] Task started: Blastn
[2024-01-24 13:57:39,220] [INFO] Running command: blastn -query GCF_002310815.1_ASM231081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd81468e0-b0a4-45bc-9563-df8b8ccb54f9/dqc_reference/reference_markers.fasta -out GCF_002310815.1_ASM231081v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:39,979] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:39,982] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:39,983] [INFO] Target genome list was writen to GCF_002310815.1_ASM231081v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:39,989] [INFO] Task started: fastANI
[2024-01-24 13:57:39,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5935a0f-4a33-4bd1-b497-c7001c3b452d/GCF_002310815.1_ASM231081v1_genomic.fna.gz --refList GCF_002310815.1_ASM231081v1_genomic.fna/target_genomes.txt --output GCF_002310815.1_ASM231081v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:52,640] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:52,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd81468e0-b0a4-45bc-9563-df8b8ccb54f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:52,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd81468e0-b0a4-45bc-9563-df8b8ccb54f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:52,652] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:57:52,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:52,652] [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
Pseudoalteromonas tunicata	strain=D2	GCA_002310815.1	314281	314281	type	True	100.0	1652	1652	95	conclusive
Pseudoalteromonas tunicata	strain=D2	GCA_003568825.1	314281	314281	type	True	99.988	1648	1652	95	conclusive
Pseudoalteromonas tunicata	strain=D2	GCA_000153245.1	314281	314281	type	True	99.9797	1636	1652	95	conclusive
Pseudoalteromonas ulvae	strain=UL12	GCA_014925405.1	107327	107327	type	True	79.8671	624	1652	95	below_threshold
Providencia manganoxydans	strain=LLDRA6	GCA_016618195.1	2923283	2923283	type	True	79.4521	52	1652	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	78.7271	263	1652	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	78.4912	249	1652	95	below_threshold
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	78.4664	256	1652	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	78.233	240	1652	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	77.9239	223	1652	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	77.8079	266	1652	95	below_threshold
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	76.3238	80	1652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:52,654] [INFO] DFAST Taxonomy check result was written to GCF_002310815.1_ASM231081v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:52,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:52,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:52,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd81468e0-b0a4-45bc-9563-df8b8ccb54f9/dqc_reference/checkm_data
[2024-01-24 13:57:52,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:52,721] [INFO] Task started: CheckM
[2024-01-24 13:57:52,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002310815.1_ASM231081v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002310815.1_ASM231081v1_genomic.fna/checkm_input GCF_002310815.1_ASM231081v1_genomic.fna/checkm_result
[2024-01-24 13:58:30,927] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:30,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:30,958] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:30,958] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:30,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002310815.1_ASM231081v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:30,959] [INFO] Task started: Blastn
[2024-01-24 13:58:30,960] [INFO] Running command: blastn -query GCF_002310815.1_ASM231081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd81468e0-b0a4-45bc-9563-df8b8ccb54f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002310815.1_ASM231081v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:32,241] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:32,244] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:32,245] [INFO] Target genome list was writen to GCF_002310815.1_ASM231081v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:32,277] [INFO] Task started: fastANI
[2024-01-24 13:58:32,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5935a0f-4a33-4bd1-b497-c7001c3b452d/GCF_002310815.1_ASM231081v1_genomic.fna.gz --refList GCF_002310815.1_ASM231081v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002310815.1_ASM231081v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:49,286] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:49,310] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:49,311] [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_002310815.1	s__Pseudoalteromonas tunicata	100.0	1651	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.99	99.99	0.99	0.99	3	conclusive
GCF_014925405.1	s__Pseudoalteromonas ulvae	79.8724	623	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.81	98.81	0.93	0.93	2	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	78.7872	256	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCF_000238395.3	s__Pseudoalteromonas arctica	78.7715	261	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	78.668	243	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	78.6321	251	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_001465295.1	s__Pseudoalteromonas translucida	78.5201	251	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	N/A	N/A	N/A	N/A	1	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	78.4959	244	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCF_012927645.1	s__Pseudoalteromonas arctica_A	78.2641	267	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469215.1	s__Pseudoalteromonas sp001469215	78.1572	255	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238335.3	s__Pseudoalteromonas marina	78.1141	229	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	97.57	0.91	0.88	12	-
GCF_000788395.1	s__Pseudoalteromonas piratica	77.9495	233	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	77.9075	253	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000238355.1	s__Pseudoalteromonas haloplanktis	77.8975	261	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.55	99.12	0.96	0.93	3	-
GCF_002165575.1	s__Pseudoalteromonas sp002165575	77.8813	259	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	77.8236	264	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_000498095.1	s__Pseudoalteromonas sp000498095	77.7837	249	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.86	97.76	0.88	0.87	3	-
GCF_002723455.1	s__Pseudoalteromonas sp002723455	77.7266	237	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.50	98.50	0.93	0.93	2	-
GCF_018100905.1	s__Pseudoalteromonas sp018100905	77.6754	217	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116435.1	s__Pseudoalteromonas lipolytica	77.669	232	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:49,318] [INFO] GTDB search result was written to GCF_002310815.1_ASM231081v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:49,325] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:49,335] [INFO] DFAST_QC result json was written to GCF_002310815.1_ASM231081v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:49,335] [INFO] DFAST_QC completed!
[2024-01-24 13:58:49,335] [INFO] Total running time: 0h1m22s