[2024-01-25 20:13:50,552] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:50,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:50,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a1821b6-1aee-4911-8f67-1f0bd70bcfaf/dqc_reference
[2024-01-25 20:13:51,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:51,777] [INFO] Task started: Prodigal
[2024-01-25 20:13:51,778] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dfcfdf1-77a5-490a-b0c0-8cd26293ef86/GCF_002270465.1_ASM227046v1_genomic.fna.gz | prodigal -d GCF_002270465.1_ASM227046v1_genomic.fna/cds.fna -a GCF_002270465.1_ASM227046v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:05,825] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:05,826] [INFO] Task started: HMMsearch
[2024-01-25 20:14:05,826] [INFO] Running command: hmmsearch --tblout GCF_002270465.1_ASM227046v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a1821b6-1aee-4911-8f67-1f0bd70bcfaf/dqc_reference/reference_markers.hmm GCF_002270465.1_ASM227046v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:06,196] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:06,197] [INFO] Found 6/6 markers.
[2024-01-25 20:14:06,243] [INFO] Query marker FASTA was written to GCF_002270465.1_ASM227046v1_genomic.fna/markers.fasta
[2024-01-25 20:14:06,243] [INFO] Task started: Blastn
[2024-01-25 20:14:06,243] [INFO] Running command: blastn -query GCF_002270465.1_ASM227046v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a1821b6-1aee-4911-8f67-1f0bd70bcfaf/dqc_reference/reference_markers.fasta -out GCF_002270465.1_ASM227046v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:06,864] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:06,873] [INFO] Selected 15 target genomes.
[2024-01-25 20:14:06,874] [INFO] Target genome list was writen to GCF_002270465.1_ASM227046v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:06,878] [INFO] Task started: fastANI
[2024-01-25 20:14:06,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dfcfdf1-77a5-490a-b0c0-8cd26293ef86/GCF_002270465.1_ASM227046v1_genomic.fna.gz --refList GCF_002270465.1_ASM227046v1_genomic.fna/target_genomes.txt --output GCF_002270465.1_ASM227046v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:19,868] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:19,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a1821b6-1aee-4911-8f67-1f0bd70bcfaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:19,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a1821b6-1aee-4911-8f67-1f0bd70bcfaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:19,877] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:19,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:19,877] [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
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	98.4654	1669	1946	95	conclusive
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	94.0666	1259	1946	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	94.0204	1263	1946	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	94.0136	1265	1946	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	85.055	1306	1946	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	84.9468	1280	1946	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	77.5404	89	1946	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	77.4505	89	1946	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.1334	116	1946	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	76.8504	69	1946	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.4543	62	1946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:19,891] [INFO] DFAST Taxonomy check result was written to GCF_002270465.1_ASM227046v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:19,892] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:19,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:19,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a1821b6-1aee-4911-8f67-1f0bd70bcfaf/dqc_reference/checkm_data
[2024-01-25 20:14:19,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:19,951] [INFO] Task started: CheckM
[2024-01-25 20:14:19,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002270465.1_ASM227046v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002270465.1_ASM227046v1_genomic.fna/checkm_input GCF_002270465.1_ASM227046v1_genomic.fna/checkm_result
[2024-01-25 20:15:01,013] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:01,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:01,032] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:01,033] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:01,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002270465.1_ASM227046v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:01,033] [INFO] Task started: Blastn
[2024-01-25 20:15:01,033] [INFO] Running command: blastn -query GCF_002270465.1_ASM227046v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a1821b6-1aee-4911-8f67-1f0bd70bcfaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_002270465.1_ASM227046v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:02,027] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:02,030] [INFO] Selected 14 target genomes.
[2024-01-25 20:15:02,031] [INFO] Target genome list was writen to GCF_002270465.1_ASM227046v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:02,038] [INFO] Task started: fastANI
[2024-01-25 20:15:02,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dfcfdf1-77a5-490a-b0c0-8cd26293ef86/GCF_002270465.1_ASM227046v1_genomic.fna.gz --refList GCF_002270465.1_ASM227046v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002270465.1_ASM227046v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:13,124] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:13,130] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:13,130] [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
GCA_002270465.1	s__Blautia hominis	100.0	1945	1946	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.84	98.04	0.89	0.81	4	conclusive
GCF_001689125.2	s__Blautia pseudococcoides	94.005	1264	1946	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.82	99.56	0.97	0.91	7	-
GCF_900461125.1	s__Blautia coccoides	85.0918	1304	1946	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.33	97.47	0.84	0.79	11	-
GCF_014287615.1	s__Blautia sp001304935	85.0062	1294	1946	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.32	98.73	0.92	0.87	9	-
GCA_003481745.1	s__Blautia stercoris	78.3142	183	1946	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.69	97.83	0.91	0.84	8	-
GCA_019119975.1	s__Blautia merdavium	77.3252	233	1946	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112785.1	s__Blautia stercorigallinarum	77.322	207	1946	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.88	99.88	0.94	0.94	2	-
GCA_900765525.1	s__Blautia pullicola	77.2382	196	1946	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.10	98.67	0.84	0.76	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:13,132] [INFO] GTDB search result was written to GCF_002270465.1_ASM227046v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:13,132] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:13,135] [INFO] DFAST_QC result json was written to GCF_002270465.1_ASM227046v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:13,135] [INFO] DFAST_QC completed!
[2024-01-25 20:15:13,135] [INFO] Total running time: 0h1m23s