[2024-01-24 14:28:02,480] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ef0ecab-bbd3-4e53-98dc-061d80cd6e21/dqc_reference
[2024-01-24 14:28:03,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:03,770] [INFO] Task started: Prodigal
[2024-01-24 14:28:03,771] [INFO] Running command: gunzip -c /var/lib/cwl/stg80d63fd5-ae4a-4ab3-81a8-e620cacf90d3/GCF_000422645.1_ASM42264v1_genomic.fna.gz | prodigal -d GCF_000422645.1_ASM42264v1_genomic.fna/cds.fna -a GCF_000422645.1_ASM42264v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:16,247] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:16,248] [INFO] Task started: HMMsearch
[2024-01-24 14:28:16,248] [INFO] Running command: hmmsearch --tblout GCF_000422645.1_ASM42264v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ef0ecab-bbd3-4e53-98dc-061d80cd6e21/dqc_reference/reference_markers.hmm GCF_000422645.1_ASM42264v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:16,640] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:16,642] [INFO] Found 6/6 markers.
[2024-01-24 14:28:16,685] [INFO] Query marker FASTA was written to GCF_000422645.1_ASM42264v1_genomic.fna/markers.fasta
[2024-01-24 14:28:16,686] [INFO] Task started: Blastn
[2024-01-24 14:28:16,686] [INFO] Running command: blastn -query GCF_000422645.1_ASM42264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ef0ecab-bbd3-4e53-98dc-061d80cd6e21/dqc_reference/reference_markers.fasta -out GCF_000422645.1_ASM42264v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:17,716] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:17,720] [INFO] Selected 11 target genomes.
[2024-01-24 14:28:17,720] [INFO] Target genome list was writen to GCF_000422645.1_ASM42264v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:17,732] [INFO] Task started: fastANI
[2024-01-24 14:28:17,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg80d63fd5-ae4a-4ab3-81a8-e620cacf90d3/GCF_000422645.1_ASM42264v1_genomic.fna.gz --refList GCF_000422645.1_ASM42264v1_genomic.fna/target_genomes.txt --output GCF_000422645.1_ASM42264v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:27,838] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:27,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ef0ecab-bbd3-4e53-98dc-061d80cd6e21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:27,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ef0ecab-bbd3-4e53-98dc-061d80cd6e21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:27,850] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:27,851] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:27,851] [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 futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	100.0	1411	1412	95	conclusive
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	85.7486	1085	1412	95	below_threshold
Ferrimonas sediminum	strain=DSM 23317	GCA_900100175.1	718193	718193	type	True	80.911	851	1412	95	below_threshold
Ferrimonas kyonanensis	strain=DSM 18153	GCA_000425405.1	364763	364763	type	True	80.4512	854	1412	95	below_threshold
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	78.899	444	1412	95	below_threshold
Ferrimonas aestuarii	strain=IMCC35002	GCA_005116665.1	2569539	2569539	type	True	78.539	446	1412	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	77.3793	147	1412	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	76.5436	109	1412	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	76.4633	173	1412	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.4263	123	1412	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	76.2428	166	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:27,853] [INFO] DFAST Taxonomy check result was written to GCF_000422645.1_ASM42264v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:27,853] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:27,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:27,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ef0ecab-bbd3-4e53-98dc-061d80cd6e21/dqc_reference/checkm_data
[2024-01-24 14:28:27,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:27,902] [INFO] Task started: CheckM
[2024-01-24 14:28:27,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422645.1_ASM42264v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422645.1_ASM42264v1_genomic.fna/checkm_input GCF_000422645.1_ASM42264v1_genomic.fna/checkm_result
[2024-01-24 14:29:09,050] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:09,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:09,072] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:09,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:09,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422645.1_ASM42264v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:09,074] [INFO] Task started: Blastn
[2024-01-24 14:29:09,074] [INFO] Running command: blastn -query GCF_000422645.1_ASM42264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ef0ecab-bbd3-4e53-98dc-061d80cd6e21/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422645.1_ASM42264v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:10,509] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:10,512] [INFO] Selected 6 target genomes.
[2024-01-24 14:29:10,512] [INFO] Target genome list was writen to GCF_000422645.1_ASM42264v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:10,521] [INFO] Task started: fastANI
[2024-01-24 14:29:10,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg80d63fd5-ae4a-4ab3-81a8-e620cacf90d3/GCF_000422645.1_ASM42264v1_genomic.fna.gz --refList GCF_000422645.1_ASM42264v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422645.1_ASM42264v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:16,516] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:16,528] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:16,528] [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_000422645.1	s__Ferrimonas futtsuensis	100.0	1411	1412	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_005116715.1	s__Ferrimonas sp005116715	85.7407	1086	1412	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	80.9264	849	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425405.1	s__Ferrimonas kyonanensis	80.4455	855	1412	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	78.8637	448	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005116665.1	s__Ferrimonas sp005116665	78.5123	449	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:16,531] [INFO] GTDB search result was written to GCF_000422645.1_ASM42264v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:16,531] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:16,534] [INFO] DFAST_QC result json was written to GCF_000422645.1_ASM42264v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:16,534] [INFO] DFAST_QC completed!
[2024-01-24 14:29:16,534] [INFO] Total running time: 0h1m14s