[2023-06-13 09:11:37,705] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:11:37,708] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:11:37,708] [INFO] DQC Reference Directory: /var/lib/cwl/stgef79e1fe-8895-405c-bc5e-8df68ef5ad17/dqc_reference
[2023-06-13 09:11:39,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:11:39,027] [INFO] Task started: Prodigal
[2023-06-13 09:11:39,027] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2fef85a-09da-4274-8022-e270f4579e0d/GCA_022009955.1_ASM2200995v1_genomic.fna.gz | prodigal -d GCA_022009955.1_ASM2200995v1_genomic.fna/cds.fna -a GCA_022009955.1_ASM2200995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:11:58,776] [INFO] Task succeeded: Prodigal
[2023-06-13 09:11:58,777] [INFO] Task started: HMMsearch
[2023-06-13 09:11:58,777] [INFO] Running command: hmmsearch --tblout GCA_022009955.1_ASM2200995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef79e1fe-8895-405c-bc5e-8df68ef5ad17/dqc_reference/reference_markers.hmm GCA_022009955.1_ASM2200995v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:11:59,013] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:11:59,014] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc2fef85a-09da-4274-8022-e270f4579e0d/GCA_022009955.1_ASM2200995v1_genomic.fna.gz]
[2023-06-13 09:11:59,045] [INFO] Query marker FASTA was written to GCA_022009955.1_ASM2200995v1_genomic.fna/markers.fasta
[2023-06-13 09:11:59,045] [INFO] Task started: Blastn
[2023-06-13 09:11:59,046] [INFO] Running command: blastn -query GCA_022009955.1_ASM2200995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef79e1fe-8895-405c-bc5e-8df68ef5ad17/dqc_reference/reference_markers.fasta -out GCA_022009955.1_ASM2200995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:11:59,622] [INFO] Task succeeded: Blastn
[2023-06-13 09:11:59,627] [INFO] Selected 18 target genomes.
[2023-06-13 09:11:59,627] [INFO] Target genome list was writen to GCA_022009955.1_ASM2200995v1_genomic.fna/target_genomes.txt
[2023-06-13 09:11:59,630] [INFO] Task started: fastANI
[2023-06-13 09:11:59,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2fef85a-09da-4274-8022-e270f4579e0d/GCA_022009955.1_ASM2200995v1_genomic.fna.gz --refList GCA_022009955.1_ASM2200995v1_genomic.fna/target_genomes.txt --output GCA_022009955.1_ASM2200995v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:12:08,474] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:08,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef79e1fe-8895-405c-bc5e-8df68ef5ad17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:12:08,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef79e1fe-8895-405c-bc5e-8df68ef5ad17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:12:08,477] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:12:08,478] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 09:12:08,478] [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
--------------------------------------------------------------------------------
[2023-06-13 09:12:08,480] [INFO] DFAST Taxonomy check result was written to GCA_022009955.1_ASM2200995v1_genomic.fna/tc_result.tsv
[2023-06-13 09:12:08,480] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:12:08,481] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:12:08,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef79e1fe-8895-405c-bc5e-8df68ef5ad17/dqc_reference/checkm_data
[2023-06-13 09:12:08,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:12:08,521] [INFO] Task started: CheckM
[2023-06-13 09:12:08,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022009955.1_ASM2200995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022009955.1_ASM2200995v1_genomic.fna/checkm_input GCA_022009955.1_ASM2200995v1_genomic.fna/checkm_result
[2023-06-13 09:13:05,265] [INFO] Task succeeded: CheckM
[2023-06-13 09:13:05,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:13:05,292] [INFO] ===== Completeness check finished =====
[2023-06-13 09:13:05,293] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:13:05,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022009955.1_ASM2200995v1_genomic.fna/markers.fasta)
[2023-06-13 09:13:05,294] [INFO] Task started: Blastn
[2023-06-13 09:13:05,294] [INFO] Running command: blastn -query GCA_022009955.1_ASM2200995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef79e1fe-8895-405c-bc5e-8df68ef5ad17/dqc_reference/reference_markers_gtdb.fasta -out GCA_022009955.1_ASM2200995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:13:06,050] [INFO] Task succeeded: Blastn
[2023-06-13 09:13:06,054] [INFO] Selected 18 target genomes.
[2023-06-13 09:13:06,054] [INFO] Target genome list was writen to GCA_022009955.1_ASM2200995v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:13:06,061] [INFO] Task started: fastANI
[2023-06-13 09:13:06,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2fef85a-09da-4274-8022-e270f4579e0d/GCA_022009955.1_ASM2200995v1_genomic.fna.gz --refList GCA_022009955.1_ASM2200995v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022009955.1_ASM2200995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:13:15,140] [INFO] Task succeeded: fastANI
[2023-06-13 09:13:15,158] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:13:15,158] [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
GCA_004557565.1	s__Sodaliphilus sp004557565	95.5478	731	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.84	96.54	0.87	0.65	13	conclusive
GCA_004563195.1	s__SFTJ01 sp004563195	82.4989	129	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004559845.1	s__Sodaliphilus sp004559845	79.9357	275	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.70	97.51	0.74	0.68	3	-
GCA_002476625.1	s__Sodaliphilus sp002476625	79.9259	403	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210415.1	s__SFTJ01 sp905210415	77.5911	96	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557385.1	s__SFTJ01 sp004557385	77.4418	98	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	97.97	96.18	0.87	0.82	3	-
GCA_900770215.1	s__Sodaliphilus sp900770215	76.9686	127	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314215.1	s__Sodaliphilus sp900314215	76.8305	161	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017619355.1	s__Sodaliphilus sp017619355	76.798	129	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318065.1	s__Sodaliphilus sp900318065	76.7931	93	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.54	97.91	0.91	0.84	24	-
GCA_016287065.1	s__Sodaliphilus sp016287065	76.7729	94	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233845.1	s__Sodaliphilus sp905233845	76.447	76	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776835.1	s__Sodaliphilus sp902776835	76.4082	123	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.85	97.41	0.91	0.88	8	-
GCA_017548365.1	s__Sodaliphilus sp017548365	76.2623	67	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792435.1	s__Sodaliphilus sp902792435	76.1787	76	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	96.75	96.43	0.87	0.84	5	-
GCA_900318535.1	s__Sodaliphilus sp900318535	75.8198	72	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.25	96.02	0.89	0.86	17	-
GCA_018065665.1	s__Sodaliphilus sp018065665	75.6603	64	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:13:15,160] [INFO] GTDB search result was written to GCA_022009955.1_ASM2200995v1_genomic.fna/result_gtdb.tsv
[2023-06-13 09:13:15,161] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:13:15,164] [INFO] DFAST_QC result json was written to GCA_022009955.1_ASM2200995v1_genomic.fna/dqc_result.json
[2023-06-13 09:13:15,164] [INFO] DFAST_QC completed!
[2023-06-13 09:13:15,164] [INFO] Total running time: 0h1m37s