[2024-01-25 18:46:35,415] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:35,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:35,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg39319837-098c-4049-8bc1-257d3becae6e/dqc_reference
[2024-01-25 18:46:36,578] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:36,579] [INFO] Task started: Prodigal
[2024-01-25 18:46:36,579] [INFO] Running command: gunzip -c /var/lib/cwl/stgf23bd5c1-1e3a-49f9-a3c0-f9ced127801c/GCF_002300555.2_ASM230055v2_genomic.fna.gz | prodigal -d GCF_002300555.2_ASM230055v2_genomic.fna/cds.fna -a GCF_002300555.2_ASM230055v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:50,666] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:50,667] [INFO] Task started: HMMsearch
[2024-01-25 18:46:50,667] [INFO] Running command: hmmsearch --tblout GCF_002300555.2_ASM230055v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39319837-098c-4049-8bc1-257d3becae6e/dqc_reference/reference_markers.hmm GCF_002300555.2_ASM230055v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:51,027] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:51,028] [INFO] Found 6/6 markers.
[2024-01-25 18:46:51,074] [INFO] Query marker FASTA was written to GCF_002300555.2_ASM230055v2_genomic.fna/markers.fasta
[2024-01-25 18:46:51,075] [INFO] Task started: Blastn
[2024-01-25 18:46:51,075] [INFO] Running command: blastn -query GCF_002300555.2_ASM230055v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg39319837-098c-4049-8bc1-257d3becae6e/dqc_reference/reference_markers.fasta -out GCF_002300555.2_ASM230055v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:52,075] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:52,079] [INFO] Selected 12 target genomes.
[2024-01-25 18:46:52,080] [INFO] Target genome list was writen to GCF_002300555.2_ASM230055v2_genomic.fna/target_genomes.txt
[2024-01-25 18:46:52,086] [INFO] Task started: fastANI
[2024-01-25 18:46:52,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgf23bd5c1-1e3a-49f9-a3c0-f9ced127801c/GCF_002300555.2_ASM230055v2_genomic.fna.gz --refList GCF_002300555.2_ASM230055v2_genomic.fna/target_genomes.txt --output GCF_002300555.2_ASM230055v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:04,602] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:04,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39319837-098c-4049-8bc1-257d3becae6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:04,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39319837-098c-4049-8bc1-257d3becae6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:04,613] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:47:04,613] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:47:04,613] [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
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	89.403	1365	1769	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	89.3843	1371	1769	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	82.8064	959	1769	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	82.3765	975	1769	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	82.0882	912	1769	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	82.0142	899	1769	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	80.8631	890	1769	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	80.6096	725	1769	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.8163	650	1769	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.7816	499	1769	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.5414	510	1769	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.942	399	1769	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:04,615] [INFO] DFAST Taxonomy check result was written to GCF_002300555.2_ASM230055v2_genomic.fna/tc_result.tsv
[2024-01-25 18:47:04,617] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:04,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:04,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39319837-098c-4049-8bc1-257d3becae6e/dqc_reference/checkm_data
[2024-01-25 18:47:04,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:04,676] [INFO] Task started: CheckM
[2024-01-25 18:47:04,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002300555.2_ASM230055v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002300555.2_ASM230055v2_genomic.fna/checkm_input GCF_002300555.2_ASM230055v2_genomic.fna/checkm_result
[2024-01-25 18:47:51,989] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:51,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:52,017] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:52,018] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:52,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002300555.2_ASM230055v2_genomic.fna/markers.fasta)
[2024-01-25 18:47:52,018] [INFO] Task started: Blastn
[2024-01-25 18:47:52,018] [INFO] Running command: blastn -query GCF_002300555.2_ASM230055v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg39319837-098c-4049-8bc1-257d3becae6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002300555.2_ASM230055v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:53,728] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:53,731] [INFO] Selected 5 target genomes.
[2024-01-25 18:47:53,731] [INFO] Target genome list was writen to GCF_002300555.2_ASM230055v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:53,736] [INFO] Task started: fastANI
[2024-01-25 18:47:53,736] [INFO] Running command: fastANI --query /var/lib/cwl/stgf23bd5c1-1e3a-49f9-a3c0-f9ced127801c/GCF_002300555.2_ASM230055v2_genomic.fna.gz --refList GCF_002300555.2_ASM230055v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002300555.2_ASM230055v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:00,888] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:00,893] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:00,893] [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_002300555.1	s__Salipiger sp002300555	99.5531	1247	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003111685.1	s__Salipiger pacificus_A	91.0267	1398	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_015223355.1	s__Salipiger pacificus_B	89.5332	1425	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	89.4039	1365	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001687105.1	s__Salipiger sp001687105	86.5297	1197	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:00,894] [INFO] GTDB search result was written to GCF_002300555.2_ASM230055v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:00,895] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:00,897] [INFO] DFAST_QC result json was written to GCF_002300555.2_ASM230055v2_genomic.fna/dqc_result.json
[2024-01-25 18:48:00,898] [INFO] DFAST_QC completed!
[2024-01-25 18:48:00,898] [INFO] Total running time: 0h1m25s