[2024-01-25 19:09:20,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:20,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:20,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e45a4f0-d6d1-4750-be8e-fc2d7ec7f919/dqc_reference
[2024-01-25 19:09:21,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:21,807] [INFO] Task started: Prodigal
[2024-01-25 19:09:21,807] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb0394bc-50d1-414f-85ae-4f888b34478c/GCF_028416595.1_ASM2841659v1_genomic.fna.gz | prodigal -d GCF_028416595.1_ASM2841659v1_genomic.fna/cds.fna -a GCF_028416595.1_ASM2841659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:28,299] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:28,299] [INFO] Task started: HMMsearch
[2024-01-25 19:09:28,299] [INFO] Running command: hmmsearch --tblout GCF_028416595.1_ASM2841659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e45a4f0-d6d1-4750-be8e-fc2d7ec7f919/dqc_reference/reference_markers.hmm GCF_028416595.1_ASM2841659v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:28,532] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:28,533] [INFO] Found 6/6 markers.
[2024-01-25 19:09:28,562] [INFO] Query marker FASTA was written to GCF_028416595.1_ASM2841659v1_genomic.fna/markers.fasta
[2024-01-25 19:09:28,562] [INFO] Task started: Blastn
[2024-01-25 19:09:28,562] [INFO] Running command: blastn -query GCF_028416595.1_ASM2841659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e45a4f0-d6d1-4750-be8e-fc2d7ec7f919/dqc_reference/reference_markers.fasta -out GCF_028416595.1_ASM2841659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:29,113] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:29,116] [INFO] Selected 24 target genomes.
[2024-01-25 19:09:29,116] [INFO] Target genome list was writen to GCF_028416595.1_ASM2841659v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:29,123] [INFO] Task started: fastANI
[2024-01-25 19:09:29,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb0394bc-50d1-414f-85ae-4f888b34478c/GCF_028416595.1_ASM2841659v1_genomic.fna.gz --refList GCF_028416595.1_ASM2841659v1_genomic.fna/target_genomes.txt --output GCF_028416595.1_ASM2841659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:43,377] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:43,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e45a4f0-d6d1-4750-be8e-fc2d7ec7f919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:43,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e45a4f0-d6d1-4750-be8e-fc2d7ec7f919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:43,389] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:09:43,389] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:09:43,389] [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
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.927	184	1200	95	below_threshold
Paraliobacillus quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	77.7976	113	1200	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	77.7547	252	1200	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	77.7263	115	1200	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.5884	175	1200	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	77.5258	50	1200	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.4499	176	1200	95	below_threshold
Halolactibacillus alkaliphilus	strain=CGMCC 1.6843	GCA_014645215.1	442899	442899	type	True	77.4498	56	1200	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.3604	96	1200	95	below_threshold
Radiobacillus deserti	strain=TKL69	GCA_007301515.1	2594883	2594883	type	True	77.2289	130	1200	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	77.2074	161	1200	95	below_threshold
Virgibacillus necropolis	strain=LMG 19488	GCA_002224365.1	163877	163877	type	True	77.1924	62	1200	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.072	71	1200	95	below_threshold
Halolactibacillus alkaliphilus	strain=NBRC 103919	GCA_007991355.1	442899	442899	type	True	77.0262	52	1200	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.9002	50	1200	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.8986	95	1200	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	76.8093	75	1200	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	76.7561	69	1200	95	below_threshold
Cerasibacillus terrae	strain=CC-CFT480	GCA_008039555.1	2498845	2498845	type	True	76.3455	64	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:43,391] [INFO] DFAST Taxonomy check result was written to GCF_028416595.1_ASM2841659v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:43,392] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:43,392] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:43,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e45a4f0-d6d1-4750-be8e-fc2d7ec7f919/dqc_reference/checkm_data
[2024-01-25 19:09:43,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:43,432] [INFO] Task started: CheckM
[2024-01-25 19:09:43,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028416595.1_ASM2841659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028416595.1_ASM2841659v1_genomic.fna/checkm_input GCF_028416595.1_ASM2841659v1_genomic.fna/checkm_result
[2024-01-25 19:10:07,908] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:07,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:07,953] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:07,953] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:07,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028416595.1_ASM2841659v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:07,954] [INFO] Task started: Blastn
[2024-01-25 19:10:07,954] [INFO] Running command: blastn -query GCF_028416595.1_ASM2841659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e45a4f0-d6d1-4750-be8e-fc2d7ec7f919/dqc_reference/reference_markers_gtdb.fasta -out GCF_028416595.1_ASM2841659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:08,709] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:08,713] [INFO] Selected 27 target genomes.
[2024-01-25 19:10:08,713] [INFO] Target genome list was writen to GCF_028416595.1_ASM2841659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:08,733] [INFO] Task started: fastANI
[2024-01-25 19:10:08,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb0394bc-50d1-414f-85ae-4f888b34478c/GCF_028416595.1_ASM2841659v1_genomic.fna.gz --refList GCF_028416595.1_ASM2841659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028416595.1_ASM2841659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:25,472] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:25,483] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:10:25,484] [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_003426025.1	s__Paraliobacillus_A quinghaiensis	77.7976	113	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016908325.1	s__Aquibacillus albus	77.7423	253	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870085.1	s__BH258 sp005870085	77.6054	174	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993965.1	s__Gracilibacillus sp010993965	77.5757	104	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280935.1	s__HU2P27 sp014280935	77.4499	176	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	77.3567	97	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_900115465.1	s__Halolactibacillus alkaliphilus	77.2723	55	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.99	99.98	0.99	0.99	3	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.2493	105	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649745.1	s__Aquibacillus_A halophilus	77.2471	185	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007301515.1	s__Radiobacillus deserti	77.2139	130	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224365.1	s__Virgibacillus_F necropolis	77.149	62	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111445.1	s__Ornithinibacillus limi	77.0699	79	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143085.1	s__Gracilibacillus kekensis	77.049	100	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458115.1	s__Gracilibacillus massiliensis	77.0018	113	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014207435.1	s__Salirhabdus euzebyi	76.9659	71	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salirhabdus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018916875.1	s__Virgibacillus proomii_B	76.8968	58	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014642895.1	s__Virgibacillus_E populi	76.8915	60	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	98.98	98.88	0.86	0.85	5	-
GCF_014636475.1	s__Halobacillus_A andaensis	76.881	54	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014638995.1	s__Virgibacillus_E oceani	76.8093	75	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:25,485] [INFO] GTDB search result was written to GCF_028416595.1_ASM2841659v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:25,486] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:25,489] [INFO] DFAST_QC result json was written to GCF_028416595.1_ASM2841659v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:25,489] [INFO] DFAST_QC completed!
[2024-01-25 19:10:25,489] [INFO] Total running time: 0h1m5s