[2024-01-24 13:49:30,680] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,682] [INFO] DQC Reference Directory: /var/lib/cwl/stge9c0e7c6-02e5-4094-b2b3-f411f55976ad/dqc_reference
[2024-01-24 13:49:31,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:31,977] [INFO] Task started: Prodigal
[2024-01-24 13:49:31,977] [INFO] Running command: gunzip -c /var/lib/cwl/stgac9d1714-205a-46b4-be2e-b09d4eb5c314/GCF_014199665.1_ASM1419966v1_genomic.fna.gz | prodigal -d GCF_014199665.1_ASM1419966v1_genomic.fna/cds.fna -a GCF_014199665.1_ASM1419966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:03,084] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:03,084] [INFO] Task started: HMMsearch
[2024-01-24 13:50:03,084] [INFO] Running command: hmmsearch --tblout GCF_014199665.1_ASM1419966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9c0e7c6-02e5-4094-b2b3-f411f55976ad/dqc_reference/reference_markers.hmm GCF_014199665.1_ASM1419966v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:03,524] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:03,525] [INFO] Found 6/6 markers.
[2024-01-24 13:50:03,579] [INFO] Query marker FASTA was written to GCF_014199665.1_ASM1419966v1_genomic.fna/markers.fasta
[2024-01-24 13:50:03,580] [INFO] Task started: Blastn
[2024-01-24 13:50:03,580] [INFO] Running command: blastn -query GCF_014199665.1_ASM1419966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c0e7c6-02e5-4094-b2b3-f411f55976ad/dqc_reference/reference_markers.fasta -out GCF_014199665.1_ASM1419966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:04,236] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:04,239] [INFO] Selected 11 target genomes.
[2024-01-24 13:50:04,240] [INFO] Target genome list was writen to GCF_014199665.1_ASM1419966v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:04,244] [INFO] Task started: fastANI
[2024-01-24 13:50:04,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgac9d1714-205a-46b4-be2e-b09d4eb5c314/GCF_014199665.1_ASM1419966v1_genomic.fna.gz --refList GCF_014199665.1_ASM1419966v1_genomic.fna/target_genomes.txt --output GCF_014199665.1_ASM1419966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:18,773] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:18,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9c0e7c6-02e5-4094-b2b3-f411f55976ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:18,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9c0e7c6-02e5-4094-b2b3-f411f55976ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:18,788] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:18,789] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:18,789] [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
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	100.0	2210	2211	95	conclusive
Parabacteroides faecis	strain=JCM 18682	GCA_014647375.1	1217282	1217282	type	True	99.9969	2198	2211	95	conclusive
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	84.8613	1205	2211	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	84.5029	1410	2211	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	82.3552	1128	2211	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	82.3354	1136	2211	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	82.2864	1143	2211	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	79.6553	526	2211	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	79.5596	531	2211	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	79.3841	569	2211	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	79.0316	70	2211	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:18,791] [INFO] DFAST Taxonomy check result was written to GCF_014199665.1_ASM1419966v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:18,791] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:18,791] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:18,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9c0e7c6-02e5-4094-b2b3-f411f55976ad/dqc_reference/checkm_data
[2024-01-24 13:50:18,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:18,855] [INFO] Task started: CheckM
[2024-01-24 13:50:18,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199665.1_ASM1419966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199665.1_ASM1419966v1_genomic.fna/checkm_input GCF_014199665.1_ASM1419966v1_genomic.fna/checkm_result
[2024-01-24 13:51:43,885] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:43,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:43,910] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:43,911] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:43,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199665.1_ASM1419966v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:43,911] [INFO] Task started: Blastn
[2024-01-24 13:51:43,912] [INFO] Running command: blastn -query GCF_014199665.1_ASM1419966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c0e7c6-02e5-4094-b2b3-f411f55976ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199665.1_ASM1419966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:44,753] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:44,759] [INFO] Selected 10 target genomes.
[2024-01-24 13:51:44,759] [INFO] Target genome list was writen to GCF_014199665.1_ASM1419966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:44,779] [INFO] Task started: fastANI
[2024-01-24 13:51:44,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgac9d1714-205a-46b4-be2e-b09d4eb5c314/GCF_014199665.1_ASM1419966v1_genomic.fna.gz --refList GCF_014199665.1_ASM1419966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199665.1_ASM1419966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:56,600] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:56,612] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:56,612] [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_014647375.1	s__Parabacteroides faecis	99.9969	2198	2211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.52	97.91	0.91	0.84	9	conclusive
GCF_003480915.1	s__Parabacteroides sp003480915	88.757	1332	2211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.39	97.67	0.93	0.87	5	-
GCF_900128505.1	s__Parabacteroides timonensis	84.8478	1205	2211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.14	96.11	0.85	0.79	3	-
GCF_015550595.1	s__Parabacteroides sp900540715	84.63	1219	2211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCF_000969835.1	s__Parabacteroides goldsteinii	84.5173	1407	2211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCA_905196875.1	s__Parabacteroides sp905196875	83.1956	1057	2211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969825.1	s__Parabacteroides gordonii	82.3014	1140	2211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	-
GCF_000156495.1	s__Parabacteroides johnsonii	79.4376	523	2211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:56,614] [INFO] GTDB search result was written to GCF_014199665.1_ASM1419966v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:56,615] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:56,618] [INFO] DFAST_QC result json was written to GCF_014199665.1_ASM1419966v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:56,618] [INFO] DFAST_QC completed!
[2024-01-24 13:51:56,618] [INFO] Total running time: 0h2m26s