[2024-01-24 10:57:07,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:07,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:07,086] [INFO] DQC Reference Directory: /var/lib/cwl/stgdffd8c15-8c75-4c7e-aaa7-e300c68709e1/dqc_reference
[2024-01-24 10:57:08,334] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:08,335] [INFO] Task started: Prodigal
[2024-01-24 10:57:08,335] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ef1e066-aac4-4451-b4f7-46ad0ccefed8/GCF_003634585.1_ASM363458v1_genomic.fna.gz | prodigal -d GCF_003634585.1_ASM363458v1_genomic.fna/cds.fna -a GCF_003634585.1_ASM363458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:19,780] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:19,781] [INFO] Task started: HMMsearch
[2024-01-24 10:57:19,781] [INFO] Running command: hmmsearch --tblout GCF_003634585.1_ASM363458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdffd8c15-8c75-4c7e-aaa7-e300c68709e1/dqc_reference/reference_markers.hmm GCF_003634585.1_ASM363458v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:20,068] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:20,069] [INFO] Found 6/6 markers.
[2024-01-24 10:57:20,104] [INFO] Query marker FASTA was written to GCF_003634585.1_ASM363458v1_genomic.fna/markers.fasta
[2024-01-24 10:57:20,105] [INFO] Task started: Blastn
[2024-01-24 10:57:20,105] [INFO] Running command: blastn -query GCF_003634585.1_ASM363458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdffd8c15-8c75-4c7e-aaa7-e300c68709e1/dqc_reference/reference_markers.fasta -out GCF_003634585.1_ASM363458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:20,774] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:20,778] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:20,778] [INFO] Target genome list was writen to GCF_003634585.1_ASM363458v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:20,785] [INFO] Task started: fastANI
[2024-01-24 10:57:20,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef1e066-aac4-4451-b4f7-46ad0ccefed8/GCF_003634585.1_ASM363458v1_genomic.fna.gz --refList GCF_003634585.1_ASM363458v1_genomic.fna/target_genomes.txt --output GCF_003634585.1_ASM363458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:31,277] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:31,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdffd8c15-8c75-4c7e-aaa7-e300c68709e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:31,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdffd8c15-8c75-4c7e-aaa7-e300c68709e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:31,291] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:31,291] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:31,292] [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
Gillisia mitskevichiae	strain=DSM 19839	GCA_003634585.1	270921	270921	type	True	100.0	1184	1186	95	conclusive
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	84.4213	815	1186	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	82.9302	702	1186	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	79.2791	134	1186	95	below_threshold
Gillisia limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	78.0762	318	1186	95	below_threshold
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	77.8339	210	1186	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	77.2256	208	1186	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	77.1032	187	1186	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	77.0541	194	1186	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	76.9501	141	1186	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.6499	76	1186	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	76.5863	100	1186	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	76.5829	98	1186	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.4861	103	1186	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.3102	79	1186	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.0606	104	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:31,294] [INFO] DFAST Taxonomy check result was written to GCF_003634585.1_ASM363458v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:31,294] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:31,295] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:31,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdffd8c15-8c75-4c7e-aaa7-e300c68709e1/dqc_reference/checkm_data
[2024-01-24 10:57:31,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:31,335] [INFO] Task started: CheckM
[2024-01-24 10:57:31,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634585.1_ASM363458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634585.1_ASM363458v1_genomic.fna/checkm_input GCF_003634585.1_ASM363458v1_genomic.fna/checkm_result
[2024-01-24 10:58:08,038] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:08,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:08,064] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:08,064] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:08,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634585.1_ASM363458v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:08,065] [INFO] Task started: Blastn
[2024-01-24 10:58:08,065] [INFO] Running command: blastn -query GCF_003634585.1_ASM363458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdffd8c15-8c75-4c7e-aaa7-e300c68709e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634585.1_ASM363458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:08,952] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:08,957] [INFO] Selected 6 target genomes.
[2024-01-24 10:58:08,957] [INFO] Target genome list was writen to GCF_003634585.1_ASM363458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:08,963] [INFO] Task started: fastANI
[2024-01-24 10:58:08,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef1e066-aac4-4451-b4f7-46ad0ccefed8/GCF_003634585.1_ASM363458v1_genomic.fna.gz --refList GCF_003634585.1_ASM363458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634585.1_ASM363458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:14,172] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:14,182] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:14,182] [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_003634585.1	s__Gillisia mitskevichiae	100.0	1184	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000403785.1	s__Gillisia sp000403785	84.9751	842	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997295.1	s__Gillisia hiemivivida	84.4258	812	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
GCF_000258765.1	s__Gillisia marina	82.9141	704	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827275.1	s__Gillisia sp007827275	82.6233	757	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364325.1	s__Gillisia sp002364325	81.6067	500	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:14,184] [INFO] GTDB search result was written to GCF_003634585.1_ASM363458v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:14,184] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:14,188] [INFO] DFAST_QC result json was written to GCF_003634585.1_ASM363458v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:14,188] [INFO] DFAST_QC completed!
[2024-01-24 10:58:14,188] [INFO] Total running time: 0h1m7s