[2024-01-24 12:47:49,675] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:49,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:49,677] [INFO] DQC Reference Directory: /var/lib/cwl/stgee478544-d24d-4930-99df-95d3a4822620/dqc_reference
[2024-01-24 12:47:50,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:50,903] [INFO] Task started: Prodigal
[2024-01-24 12:47:50,903] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cf669af-9d77-4b39-9c1c-10702fa0bb9b/GCF_019734885.1_ASM1973488v1_genomic.fna.gz | prodigal -d GCF_019734885.1_ASM1973488v1_genomic.fna/cds.fna -a GCF_019734885.1_ASM1973488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:59,716] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:59,717] [INFO] Task started: HMMsearch
[2024-01-24 12:47:59,717] [INFO] Running command: hmmsearch --tblout GCF_019734885.1_ASM1973488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee478544-d24d-4930-99df-95d3a4822620/dqc_reference/reference_markers.hmm GCF_019734885.1_ASM1973488v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:59,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:59,975] [INFO] Found 6/6 markers.
[2024-01-24 12:48:00,011] [INFO] Query marker FASTA was written to GCF_019734885.1_ASM1973488v1_genomic.fna/markers.fasta
[2024-01-24 12:48:00,011] [INFO] Task started: Blastn
[2024-01-24 12:48:00,012] [INFO] Running command: blastn -query GCF_019734885.1_ASM1973488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee478544-d24d-4930-99df-95d3a4822620/dqc_reference/reference_markers.fasta -out GCF_019734885.1_ASM1973488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:00,660] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:00,666] [INFO] Selected 24 target genomes.
[2024-01-24 12:48:00,666] [INFO] Target genome list was writen to GCF_019734885.1_ASM1973488v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:00,749] [INFO] Task started: fastANI
[2024-01-24 12:48:00,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cf669af-9d77-4b39-9c1c-10702fa0bb9b/GCF_019734885.1_ASM1973488v1_genomic.fna.gz --refList GCF_019734885.1_ASM1973488v1_genomic.fna/target_genomes.txt --output GCF_019734885.1_ASM1973488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:16,040] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:16,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee478544-d24d-4930-99df-95d3a4822620/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:16,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee478544-d24d-4930-99df-95d3a4822620/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:16,062] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:48:16,062] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:16,062] [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
Coprococcus catus	strain=VPIC661	GCA_019734885.1	116085	116085	suspected-type	True	100.0	1164	1169	95	conclusive
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	99.992	1141	1169	95	conclusive
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	85.1807	80	1169	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	83.4976	99	1169	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	83.3721	104	1169	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	83.0728	97	1169	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	82.9471	172	1169	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	82.6318	165	1169	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	81.9877	89	1169	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	81.9715	124	1169	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	81.8669	89	1169	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	81.8249	87	1169	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	80.4266	54	1169	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	80.2521	79	1169	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	77.9995	56	1169	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	77.9966	56	1169	95	below_threshold
Frisingicoccus caecimuris	strain=DSM 28559	GCA_024622585.1	1796636	1796636	type	True	77.8535	103	1169	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	77.7374	53	1169	95	below_threshold
Frisingicoccus caecimuris	strain=DSM 28559	GCA_004340975.1	1796636	1796636	type	True	77.7102	104	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:16,064] [INFO] DFAST Taxonomy check result was written to GCF_019734885.1_ASM1973488v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:16,065] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:16,065] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:16,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee478544-d24d-4930-99df-95d3a4822620/dqc_reference/checkm_data
[2024-01-24 12:48:16,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:16,102] [INFO] Task started: CheckM
[2024-01-24 12:48:16,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019734885.1_ASM1973488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019734885.1_ASM1973488v1_genomic.fna/checkm_input GCF_019734885.1_ASM1973488v1_genomic.fna/checkm_result
[2024-01-24 12:48:48,078] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:48,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:48,105] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:48,106] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:48,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019734885.1_ASM1973488v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:48,107] [INFO] Task started: Blastn
[2024-01-24 12:48:48,107] [INFO] Running command: blastn -query GCF_019734885.1_ASM1973488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee478544-d24d-4930-99df-95d3a4822620/dqc_reference/reference_markers_gtdb.fasta -out GCF_019734885.1_ASM1973488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:49,222] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:49,227] [INFO] Selected 18 target genomes.
[2024-01-24 12:48:49,227] [INFO] Target genome list was writen to GCF_019734885.1_ASM1973488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:49,258] [INFO] Task started: fastANI
[2024-01-24 12:48:49,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cf669af-9d77-4b39-9c1c-10702fa0bb9b/GCF_019734885.1_ASM1973488v1_genomic.fna.gz --refList GCF_019734885.1_ASM1973488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019734885.1_ASM1973488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:57,734] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:57,758] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:57,759] [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_018785175.1	s__Coprococcus_A sp900548825	97.2932	887	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus_A	95.0	98.21	98.06	0.90	0.89	4	conclusive
GCF_902381825.1	s__Coprococcus_A catus	90.5969	788	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus_A	95.0	98.33	97.35	0.89	0.80	8	-
GCA_018223435.1	s__Limivivens sp900543575	82.7206	74	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.02	97.88	0.92	0.90	4	-
GCF_013300725.1	s__Bariatricus comes_A	80.9654	109	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCF_013304825.1	s__Blautia_A schinkii	80.4425	105	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.24	98.34	0.93	0.82	9	-
GCA_016297495.1	s__Coprococcus_A sp016297495	79.3792	314	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016298055.1	s__Frisingicoccus sp016298055	77.8445	89	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	95.75	95.75	0.73	0.73	2	-
GCF_004340975.1	s__Frisingicoccus caecimuris	77.6788	105	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	98.08	97.54	0.83	0.77	6	-
GCA_900764225.1	s__Blautia_A sp900764225	77.4865	67	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905199445.1	s__Catenibacillus sp900553975	76.9924	78	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	99.69	99.69	0.90	0.90	2	-
GCA_018716485.1	s__Scybalocola faecipullorum	76.9847	59	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scybalocola	95.0	99.49	99.00	0.90	0.85	3	-
GCA_900757195.1	s__Frisingicoccus sp900757195	76.7504	81	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.09	99.09	0.92	0.92	2	-
GCA_900549105.1	s__Frisingicoccus sp900549105	76.6835	75	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.93	99.87	0.93	0.90	3	-
GCA_902787905.1	s__UBA2912 sp902787905	76.3864	62	1169	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2912	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:57,761] [INFO] GTDB search result was written to GCF_019734885.1_ASM1973488v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:57,762] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:57,766] [INFO] DFAST_QC result json was written to GCF_019734885.1_ASM1973488v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:57,767] [INFO] DFAST_QC completed!
[2024-01-24 12:48:57,767] [INFO] Total running time: 0h1m8s