[2024-01-24 13:32:25,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:25,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:25,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgad5f895a-28f8-4295-ada5-36a649cdc848/dqc_reference
[2024-01-24 13:32:26,509] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:26,510] [INFO] Task started: Prodigal
[2024-01-24 13:32:26,510] [INFO] Running command: gunzip -c /var/lib/cwl/stgc52434f4-6cc0-4f4c-bbfb-bc4ce917cb77/GCF_005116665.1_ASM511666v1_genomic.fna.gz | prodigal -d GCF_005116665.1_ASM511666v1_genomic.fna/cds.fna -a GCF_005116665.1_ASM511666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:39,715] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:39,716] [INFO] Task started: HMMsearch
[2024-01-24 13:32:39,716] [INFO] Running command: hmmsearch --tblout GCF_005116665.1_ASM511666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad5f895a-28f8-4295-ada5-36a649cdc848/dqc_reference/reference_markers.hmm GCF_005116665.1_ASM511666v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:40,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:40,038] [INFO] Found 6/6 markers.
[2024-01-24 13:32:40,080] [INFO] Query marker FASTA was written to GCF_005116665.1_ASM511666v1_genomic.fna/markers.fasta
[2024-01-24 13:32:40,081] [INFO] Task started: Blastn
[2024-01-24 13:32:40,081] [INFO] Running command: blastn -query GCF_005116665.1_ASM511666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad5f895a-28f8-4295-ada5-36a649cdc848/dqc_reference/reference_markers.fasta -out GCF_005116665.1_ASM511666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:40,970] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:40,974] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:40,974] [INFO] Target genome list was writen to GCF_005116665.1_ASM511666v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:40,984] [INFO] Task started: fastANI
[2024-01-24 13:32:40,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgc52434f4-6cc0-4f4c-bbfb-bc4ce917cb77/GCF_005116665.1_ASM511666v1_genomic.fna.gz --refList GCF_005116665.1_ASM511666v1_genomic.fna/target_genomes.txt --output GCF_005116665.1_ASM511666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:52,380] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:52,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad5f895a-28f8-4295-ada5-36a649cdc848/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:52,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad5f895a-28f8-4295-ada5-36a649cdc848/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:52,390] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:52,391] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:52,391] [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
Ferrimonas aestuarii	strain=IMCC35002	GCA_005116665.1	2569539	2569539	type	True	100.0	1560	1562	95	conclusive
Ferrimonas kyonanensis	strain=DSM 18153	GCA_000425405.1	364763	364763	type	True	79.2476	503	1562	95	below_threshold
Ferrimonas sediminum	strain=DSM 23317	GCA_900100175.1	718193	718193	type	True	79.0507	484	1562	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	78.5606	448	1562	95	below_threshold
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	78.2682	399	1562	95	below_threshold
Ferrimonas senticii	strain=DSM 18821	GCA_000422665.1	394566	394566	type	True	77.9508	195	1562	95	below_threshold
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	77.4123	195	1562	95	below_threshold
Ferrimonas marina	strain=NBRC 102583	GCA_001571125.1	299255	299255	type	True	77.3735	180	1562	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	77.2836	120	1562	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	76.9127	69	1562	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	76.8938	108	1562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:52,392] [INFO] DFAST Taxonomy check result was written to GCF_005116665.1_ASM511666v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:52,393] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:52,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:52,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad5f895a-28f8-4295-ada5-36a649cdc848/dqc_reference/checkm_data
[2024-01-24 13:32:52,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:52,448] [INFO] Task started: CheckM
[2024-01-24 13:32:52,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005116665.1_ASM511666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005116665.1_ASM511666v1_genomic.fna/checkm_input GCF_005116665.1_ASM511666v1_genomic.fna/checkm_result
[2024-01-24 13:33:37,299] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:37,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:37,316] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:37,317] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:37,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005116665.1_ASM511666v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:37,318] [INFO] Task started: Blastn
[2024-01-24 13:33:37,318] [INFO] Running command: blastn -query GCF_005116665.1_ASM511666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad5f895a-28f8-4295-ada5-36a649cdc848/dqc_reference/reference_markers_gtdb.fasta -out GCF_005116665.1_ASM511666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:38,680] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:38,683] [INFO] Selected 11 target genomes.
[2024-01-24 13:33:38,684] [INFO] Target genome list was writen to GCF_005116665.1_ASM511666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:38,694] [INFO] Task started: fastANI
[2024-01-24 13:33:38,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgc52434f4-6cc0-4f4c-bbfb-bc4ce917cb77/GCF_005116665.1_ASM511666v1_genomic.fna.gz --refList GCF_005116665.1_ASM511666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005116665.1_ASM511666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:48,387] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:48,397] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:48,397] [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_005116665.1	s__Ferrimonas sp005116665	100.0	1560	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000425405.1	s__Ferrimonas kyonanensis	79.253	502	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100175.1	s__Ferrimonas sediminum	79.0508	482	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422645.1	s__Ferrimonas futtsuensis	78.5528	451	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116715.1	s__Ferrimonas sp005116715	78.2372	400	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422665.1	s__Ferrimonas senticii	77.9365	195	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129905.1	s__Ferrimonas marina	77.4121	194	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000819745.1	s__Aeromonas bestiarum	76.7954	83	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000820225.1	s__Aeromonas veronii	76.7104	81	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.01	0.90	0.86	159	-
GCF_000820145.1	s__Aeromonas sobria	76.7059	80	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.57	95.21	0.89	0.85	13	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:48,401] [INFO] GTDB search result was written to GCF_005116665.1_ASM511666v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:48,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:48,408] [INFO] DFAST_QC result json was written to GCF_005116665.1_ASM511666v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:48,408] [INFO] DFAST_QC completed!
[2024-01-24 13:33:48,409] [INFO] Total running time: 0h1m23s