[2024-01-24 12:07:06,352] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg632445f6-18f1-490c-b390-0dabcae2fadd/dqc_reference
[2024-01-24 12:07:07,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,614] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d22dd8b-5a5a-4e63-8b2a-53b52c14e1ef/GCF_000730385.1_ASM73038v1_genomic.fna.gz | prodigal -d GCF_000730385.1_ASM73038v1_genomic.fna/cds.fna -a GCF_000730385.1_ASM73038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:18,020] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:18,021] [INFO] Task started: HMMsearch
[2024-01-24 12:07:18,021] [INFO] Running command: hmmsearch --tblout GCF_000730385.1_ASM73038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg632445f6-18f1-490c-b390-0dabcae2fadd/dqc_reference/reference_markers.hmm GCF_000730385.1_ASM73038v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:18,381] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:18,383] [INFO] Found 6/6 markers.
[2024-01-24 12:07:18,424] [INFO] Query marker FASTA was written to GCF_000730385.1_ASM73038v1_genomic.fna/markers.fasta
[2024-01-24 12:07:18,424] [INFO] Task started: Blastn
[2024-01-24 12:07:18,424] [INFO] Running command: blastn -query GCF_000730385.1_ASM73038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg632445f6-18f1-490c-b390-0dabcae2fadd/dqc_reference/reference_markers.fasta -out GCF_000730385.1_ASM73038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:19,153] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:19,158] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:19,158] [INFO] Target genome list was writen to GCF_000730385.1_ASM73038v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:19,162] [INFO] Task started: fastANI
[2024-01-24 12:07:19,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d22dd8b-5a5a-4e63-8b2a-53b52c14e1ef/GCF_000730385.1_ASM73038v1_genomic.fna.gz --refList GCF_000730385.1_ASM73038v1_genomic.fna/target_genomes.txt --output GCF_000730385.1_ASM73038v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:29,008] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:29,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg632445f6-18f1-490c-b390-0dabcae2fadd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:29,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg632445f6-18f1-490c-b390-0dabcae2fadd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:29,018] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:29,018] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:29,018] [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
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	100.0	1435	1436	95	conclusive
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	81.9356	442	1436	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	81.807	532	1436	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	80.6293	398	1436	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	80.5526	400	1436	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	80.4098	421	1436	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	80.2993	473	1436	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	80.2197	421	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:29,019] [INFO] DFAST Taxonomy check result was written to GCF_000730385.1_ASM73038v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:29,020] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:29,020] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:29,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg632445f6-18f1-490c-b390-0dabcae2fadd/dqc_reference/checkm_data
[2024-01-24 12:07:29,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:29,061] [INFO] Task started: CheckM
[2024-01-24 12:07:29,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000730385.1_ASM73038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000730385.1_ASM73038v1_genomic.fna/checkm_input GCF_000730385.1_ASM73038v1_genomic.fna/checkm_result
[2024-01-24 12:08:04,540] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:04,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:04,563] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:04,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:04,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000730385.1_ASM73038v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:04,564] [INFO] Task started: Blastn
[2024-01-24 12:08:04,564] [INFO] Running command: blastn -query GCF_000730385.1_ASM73038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg632445f6-18f1-490c-b390-0dabcae2fadd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000730385.1_ASM73038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:05,642] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:05,646] [INFO] Selected 18 target genomes.
[2024-01-24 12:08:05,646] [INFO] Target genome list was writen to GCF_000730385.1_ASM73038v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:05,663] [INFO] Task started: fastANI
[2024-01-24 12:08:05,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d22dd8b-5a5a-4e63-8b2a-53b52c14e1ef/GCF_000730385.1_ASM73038v1_genomic.fna.gz --refList GCF_000730385.1_ASM73038v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000730385.1_ASM73038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:20,489] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:20,513] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:20,513] [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_000730385.1	s__Alteromonas australica	100.0	1434	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	conclusive
GCF_000020585.3	s__Alteromonas mediterranea	81.9348	442	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCF_010500865.1	s__Alteromonas profundi	81.821	531	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506055.1	s__Alteromonas lipotrueae	80.6625	471	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCF_903772925.1	s__Alteromonas macleodii_A	80.6225	442	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993325.1	s__Alteromonas gracilis	80.594	401	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_001953635.1	s__Alteromonas abrolhosensis	80.58	402	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_000597705.1	s__Alteromonas sp000597705	80.5018	417	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_016756315.1	s__Alteromonas sp009811495	80.4769	382	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.33	96.67	0.93	0.86	3	-
GCF_016405965.1	s__Alteromonas sp016405965	80.4511	399	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172635.2	s__Alteromonas macleodii	80.4507	421	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_003443615.1	s__Alteromonas sp003443615	80.4058	426	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005117025.1	s__Alteromonas portus	80.1931	423	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808575.1	s__Alteromonas marina	80.1577	426	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_009811415.1	s__Alteromonas sp009811415	80.0199	379	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000213655.1	s__Alteromonas naphthalenivorans	79.7569	472	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	-
GCF_010500895.1	s__Alteromonas genovensis	79.531	343	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.09	98.06	0.82	0.81	3	-
GCF_000753865.1	s__Alteromonas sp000753865	79.4216	355	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:20,515] [INFO] GTDB search result was written to GCF_000730385.1_ASM73038v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:20,516] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:20,519] [INFO] DFAST_QC result json was written to GCF_000730385.1_ASM73038v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:20,519] [INFO] DFAST_QC completed!
[2024-01-24 12:08:20,519] [INFO] Total running time: 0h1m14s