[2024-01-24 13:57:16,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg751b9f74-e17f-4013-bac3-0d7d1e98b5f5/dqc_reference
[2024-01-24 13:57:17,919] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,920] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,920] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fe44dc9-a62d-43e9-89bc-2055b833860b/GCF_002285495.1_ASM228549v1_genomic.fna.gz | prodigal -d GCF_002285495.1_ASM228549v1_genomic.fna/cds.fna -a GCF_002285495.1_ASM228549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:22,305] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:22,305] [INFO] Task started: HMMsearch
[2024-01-24 13:57:22,306] [INFO] Running command: hmmsearch --tblout GCF_002285495.1_ASM228549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg751b9f74-e17f-4013-bac3-0d7d1e98b5f5/dqc_reference/reference_markers.hmm GCF_002285495.1_ASM228549v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:22,598] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:22,599] [INFO] Found 6/6 markers.
[2024-01-24 13:57:22,624] [INFO] Query marker FASTA was written to GCF_002285495.1_ASM228549v1_genomic.fna/markers.fasta
[2024-01-24 13:57:22,624] [INFO] Task started: Blastn
[2024-01-24 13:57:22,624] [INFO] Running command: blastn -query GCF_002285495.1_ASM228549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg751b9f74-e17f-4013-bac3-0d7d1e98b5f5/dqc_reference/reference_markers.fasta -out GCF_002285495.1_ASM228549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:23,249] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:23,256] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:23,257] [INFO] Target genome list was writen to GCF_002285495.1_ASM228549v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:23,266] [INFO] Task started: fastANI
[2024-01-24 13:57:23,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fe44dc9-a62d-43e9-89bc-2055b833860b/GCF_002285495.1_ASM228549v1_genomic.fna.gz --refList GCF_002285495.1_ASM228549v1_genomic.fna/target_genomes.txt --output GCF_002285495.1_ASM228549v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:34,184] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:34,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg751b9f74-e17f-4013-bac3-0d7d1e98b5f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:34,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg751b9f74-e17f-4013-bac3-0d7d1e98b5f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:34,202] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:34,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:34,202] [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
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	100.0	955	956	95	conclusive
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	79.2257	391	956	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.8445	265	956	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	78.8405	352	956	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	78.6906	416	956	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	78.6621	282	956	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	78.2573	194	956	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	77.9773	154	956	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	77.833	211	956	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	77.7418	203	956	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	77.242	174	956	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.1338	178	956	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	77.0761	241	956	95	below_threshold
Gottschalkia acidurici	strain=9a	GCA_000299355.1	1556	1556	type	True	76.0983	67	956	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	74.9054	51	956	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:34,204] [INFO] DFAST Taxonomy check result was written to GCF_002285495.1_ASM228549v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:34,205] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:34,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:34,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg751b9f74-e17f-4013-bac3-0d7d1e98b5f5/dqc_reference/checkm_data
[2024-01-24 13:57:34,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:34,237] [INFO] Task started: CheckM
[2024-01-24 13:57:34,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002285495.1_ASM228549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002285495.1_ASM228549v1_genomic.fna/checkm_input GCF_002285495.1_ASM228549v1_genomic.fna/checkm_result
[2024-01-24 13:57:54,804] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:54,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:54,824] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:54,824] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:54,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002285495.1_ASM228549v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:54,825] [INFO] Task started: Blastn
[2024-01-24 13:57:54,826] [INFO] Running command: blastn -query GCF_002285495.1_ASM228549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg751b9f74-e17f-4013-bac3-0d7d1e98b5f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002285495.1_ASM228549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:55,650] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:55,653] [INFO] Selected 12 target genomes.
[2024-01-24 13:57:55,653] [INFO] Target genome list was writen to GCF_002285495.1_ASM228549v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:55,664] [INFO] Task started: fastANI
[2024-01-24 13:57:55,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fe44dc9-a62d-43e9-89bc-2055b833860b/GCF_002285495.1_ASM228549v1_genomic.fna.gz --refList GCF_002285495.1_ASM228549v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002285495.1_ASM228549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:05,097] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:05,111] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:05,111] [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_002285495.1	s__Clostridium isatidis	100.0	954	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.19	99.19	0.81	0.81	2	conclusive
GCF_018918055.1	s__Clostridium sp018918055	91.8432	668	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520205.1	s__Clostridium sp012520205	86.3535	488	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900086595.1	s__Clostridium nigeriense	79.1771	395	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.98	98.98	0.91	0.91	2	-
GCF_000401215.1	s__Clostridium sartagoforme_A	79.0997	388	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCF_015550425.1	s__Clostridium sp015550425	78.9916	418	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.01	99.01	0.93	0.93	2	-
GCA_017888565.1	s__Clostridium sp017888565	78.9454	424	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435645.1	s__Clostridium sp017435645	78.7709	184	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873245.1	s__Clostridium tertium	78.7206	413	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCF_004794105.1	s__Clostridium sartagoforme_B	78.4598	334	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCA_018372555.1	s__Clostridium sp018372555	78.137	264	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230835.1	s__Clostridium sp000230835	77.2314	208	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.12	96.12	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:05,112] [INFO] GTDB search result was written to GCF_002285495.1_ASM228549v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:05,113] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:05,116] [INFO] DFAST_QC result json was written to GCF_002285495.1_ASM228549v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:05,116] [INFO] DFAST_QC completed!
[2024-01-24 13:58:05,117] [INFO] Total running time: 0h0m49s