[2024-01-24 14:14:01,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:01,078] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:01,078] [INFO] DQC Reference Directory: /var/lib/cwl/stga3d14215-a246-42c8-9934-acd019dea32b/dqc_reference
[2024-01-24 14:14:02,551] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:02,552] [INFO] Task started: Prodigal
[2024-01-24 14:14:02,552] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcf0fda6-09c1-4777-b24a-914542ee2be0/GCF_005780165.1_ASM578016v1_genomic.fna.gz | prodigal -d GCF_005780165.1_ASM578016v1_genomic.fna/cds.fna -a GCF_005780165.1_ASM578016v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:48,899] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:48,899] [INFO] Task started: HMMsearch
[2024-01-24 14:14:48,899] [INFO] Running command: hmmsearch --tblout GCF_005780165.1_ASM578016v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3d14215-a246-42c8-9934-acd019dea32b/dqc_reference/reference_markers.hmm GCF_005780165.1_ASM578016v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:49,231] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:49,232] [INFO] Found 6/6 markers.
[2024-01-24 14:14:49,281] [INFO] Query marker FASTA was written to GCF_005780165.1_ASM578016v1_genomic.fna/markers.fasta
[2024-01-24 14:14:49,282] [INFO] Task started: Blastn
[2024-01-24 14:14:49,282] [INFO] Running command: blastn -query GCF_005780165.1_ASM578016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3d14215-a246-42c8-9934-acd019dea32b/dqc_reference/reference_markers.fasta -out GCF_005780165.1_ASM578016v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:49,855] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:49,859] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:49,860] [INFO] Target genome list was writen to GCF_005780165.1_ASM578016v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:49,875] [INFO] Task started: fastANI
[2024-01-24 14:14:49,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcf0fda6-09c1-4777-b24a-914542ee2be0/GCF_005780165.1_ASM578016v1_genomic.fna.gz --refList GCF_005780165.1_ASM578016v1_genomic.fna/target_genomes.txt --output GCF_005780165.1_ASM578016v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:05,025] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:05,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3d14215-a246-42c8-9934-acd019dea32b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:05,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3d14215-a246-42c8-9934-acd019dea32b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:05,040] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:05,040] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:05,040] [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
Phragmitibacter flavus	strain=MG-N-17	GCA_005780165.1	2576071	2576071	type	True	100.0	1946	1948	95	conclusive
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	76.4973	163	1948	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	76.4592	153	1948	95	below_threshold
Prosthecobacter debontii	strain=ATCC 700200	GCA_900167535.1	48467	48467	type	True	76.4467	113	1948	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	76.3972	216	1948	95	below_threshold
Prosthecobacter dejongeii	strain=DSM 12251	GCA_014203045.1	48465	48465	type	True	76.3544	91	1948	95	below_threshold
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	76.3186	125	1948	95	below_threshold
Prosthecobacter fusiformis	strain=ATCC 25309	GCA_004364345.1	48464	48464	type	True	76.1976	133	1948	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:05,041] [INFO] DFAST Taxonomy check result was written to GCF_005780165.1_ASM578016v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:05,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:05,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:05,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3d14215-a246-42c8-9934-acd019dea32b/dqc_reference/checkm_data
[2024-01-24 14:15:05,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:05,115] [INFO] Task started: CheckM
[2024-01-24 14:15:05,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005780165.1_ASM578016v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005780165.1_ASM578016v1_genomic.fna/checkm_input GCF_005780165.1_ASM578016v1_genomic.fna/checkm_result
[2024-01-24 14:17:07,916] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:07,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:07,939] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:07,939] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:07,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005780165.1_ASM578016v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:07,940] [INFO] Task started: Blastn
[2024-01-24 14:17:07,940] [INFO] Running command: blastn -query GCF_005780165.1_ASM578016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3d14215-a246-42c8-9934-acd019dea32b/dqc_reference/reference_markers_gtdb.fasta -out GCF_005780165.1_ASM578016v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:08,738] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:08,741] [INFO] Selected 19 target genomes.
[2024-01-24 14:17:08,742] [INFO] Target genome list was writen to GCF_005780165.1_ASM578016v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:08,798] [INFO] Task started: fastANI
[2024-01-24 14:17:08,798] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcf0fda6-09c1-4777-b24a-914542ee2be0/GCF_005780165.1_ASM578016v1_genomic.fna.gz --refList GCF_005780165.1_ASM578016v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005780165.1_ASM578016v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:28,116] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:28,130] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:28,130] [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_005780165.1	s__Phragmitibacter flavus	100.0	1946	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Phragmitibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019186985.1	s__Prosthecobacter sp019186985	76.6367	175	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739655.1	s__Verrucomicrobium sp000739655	76.5986	189	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Verrucomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739635.1	s__Verrucomicrobium sp000739635	76.5964	207	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Verrucomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713035.1	s__Prosthecobacter sp016713035	76.5817	122	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017301975.1	s__Prosthecobacter sp017301975	76.4784	149	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713245.1	s__Prosthecobacter sp016713245	76.476	151	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011044495.1	s__Roseimicrobium sp011044495	76.4218	191	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Roseimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172155.1	s__Verrucomicrobium spinosum	76.4064	215	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Verrucomicrobium	95.0	99.88	99.88	1.00	1.00	2	-
GCA_002482965.1	s__Prosthecobacter sp002482965	76.3178	162	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364345.1	s__Prosthecobacter fusiformis	76.2507	129	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903838675.1	s__Prosthecobacter sp903838675	76.1943	148	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.92	99.91	0.96	0.96	3	-
GCA_002279765.1	s__Prosthecobacter sp002279765	76.1574	149	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960845.1	s__Prosthecobacter sp903960845	76.0274	94	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.18	98.90	0.84	0.82	4	-
GCA_005787565.1	s__Luteolibacter sp005787565	75.7192	93	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903954065.1	s__CAJBME01 sp903954065	75.6659	60	1948	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__V1-33;g__CAJBME01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:28,132] [INFO] GTDB search result was written to GCF_005780165.1_ASM578016v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:28,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:28,138] [INFO] DFAST_QC result json was written to GCF_005780165.1_ASM578016v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:28,139] [INFO] DFAST_QC completed!
[2024-01-24 14:17:28,139] [INFO] Total running time: 0h3m27s