[2024-01-25 19:02:06,093] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:06,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:06,095] [INFO] DQC Reference Directory: /var/lib/cwl/stga75b9a38-b8f9-41f9-a63a-097bd112138e/dqc_reference
[2024-01-25 19:02:07,232] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:07,232] [INFO] Task started: Prodigal
[2024-01-25 19:02:07,233] [INFO] Running command: gunzip -c /var/lib/cwl/stg144d8149-1670-4262-8dc0-95956910395e/GCF_003014435.1_ASM301443v1_genomic.fna.gz | prodigal -d GCF_003014435.1_ASM301443v1_genomic.fna/cds.fna -a GCF_003014435.1_ASM301443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:17,746] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:17,746] [INFO] Task started: HMMsearch
[2024-01-25 19:02:17,746] [INFO] Running command: hmmsearch --tblout GCF_003014435.1_ASM301443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga75b9a38-b8f9-41f9-a63a-097bd112138e/dqc_reference/reference_markers.hmm GCF_003014435.1_ASM301443v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:17,976] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:17,977] [INFO] Found 6/6 markers.
[2024-01-25 19:02:18,007] [INFO] Query marker FASTA was written to GCF_003014435.1_ASM301443v1_genomic.fna/markers.fasta
[2024-01-25 19:02:18,008] [INFO] Task started: Blastn
[2024-01-25 19:02:18,008] [INFO] Running command: blastn -query GCF_003014435.1_ASM301443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga75b9a38-b8f9-41f9-a63a-097bd112138e/dqc_reference/reference_markers.fasta -out GCF_003014435.1_ASM301443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:19,040] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:19,044] [INFO] Selected 12 target genomes.
[2024-01-25 19:02:19,044] [INFO] Target genome list was writen to GCF_003014435.1_ASM301443v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:19,061] [INFO] Task started: fastANI
[2024-01-25 19:02:19,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg144d8149-1670-4262-8dc0-95956910395e/GCF_003014435.1_ASM301443v1_genomic.fna.gz --refList GCF_003014435.1_ASM301443v1_genomic.fna/target_genomes.txt --output GCF_003014435.1_ASM301443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:29,086] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:29,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga75b9a38-b8f9-41f9-a63a-097bd112138e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:29,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga75b9a38-b8f9-41f9-a63a-097bd112138e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:29,095] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:02:29,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:29,095] [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
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	100.0	1252	1256	95	conclusive
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	99.9984	1253	1256	95	conclusive
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	87.824	889	1256	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	87.7924	883	1256	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	87.7268	876	1256	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	87.0661	897	1256	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	86.2076	894	1256	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.771	423	1256	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.6498	442	1256	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5719	428	1256	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.1407	366	1256	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.5113	336	1256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:29,096] [INFO] DFAST Taxonomy check result was written to GCF_003014435.1_ASM301443v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:29,097] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:29,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:29,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga75b9a38-b8f9-41f9-a63a-097bd112138e/dqc_reference/checkm_data
[2024-01-25 19:02:29,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:29,138] [INFO] Task started: CheckM
[2024-01-25 19:02:29,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014435.1_ASM301443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014435.1_ASM301443v1_genomic.fna/checkm_input GCF_003014435.1_ASM301443v1_genomic.fna/checkm_result
[2024-01-25 19:03:02,864] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:02,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:02,880] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:02,880] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:02,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014435.1_ASM301443v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:02,881] [INFO] Task started: Blastn
[2024-01-25 19:03:02,881] [INFO] Running command: blastn -query GCF_003014435.1_ASM301443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga75b9a38-b8f9-41f9-a63a-097bd112138e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014435.1_ASM301443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:05,008] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:05,016] [INFO] Selected 6 target genomes.
[2024-01-25 19:03:05,016] [INFO] Target genome list was writen to GCF_003014435.1_ASM301443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:05,024] [INFO] Task started: fastANI
[2024-01-25 19:03:05,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg144d8149-1670-4262-8dc0-95956910395e/GCF_003014435.1_ASM301443v1_genomic.fna.gz --refList GCF_003014435.1_ASM301443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014435.1_ASM301443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:10,977] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:10,983] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:10,983] [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_900172345.1	s__Limimaricola soesokkakensis	99.9984	1253	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014195545.1	s__Limimaricola variabilis	87.824	889	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	87.7926	883	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	87.7658	880	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466965.1	s__Limimaricola cinnabarinus	87.0661	897	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	86.2263	892	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:10,984] [INFO] GTDB search result was written to GCF_003014435.1_ASM301443v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:10,985] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:10,990] [INFO] DFAST_QC result json was written to GCF_003014435.1_ASM301443v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:10,990] [INFO] DFAST_QC completed!
[2024-01-25 19:03:10,990] [INFO] Total running time: 0h1m5s