[2023-06-13 20:24:47,186] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:24:47,188] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:24:47,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d94326b-2932-4f14-9029-6b3d3a5f6b15/dqc_reference
[2023-06-13 20:24:48,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:24:48,303] [INFO] Task started: Prodigal
[2023-06-13 20:24:48,303] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1a8461b-2df4-4790-857d-6d48fe0a37d6/GCA_022783145.1_ASM2278314v1_genomic.fna.gz | prodigal -d GCA_022783145.1_ASM2278314v1_genomic.fna/cds.fna -a GCA_022783145.1_ASM2278314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:24:52,523] [INFO] Task succeeded: Prodigal
[2023-06-13 20:24:52,523] [INFO] Task started: HMMsearch
[2023-06-13 20:24:52,523] [INFO] Running command: hmmsearch --tblout GCA_022783145.1_ASM2278314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d94326b-2932-4f14-9029-6b3d3a5f6b15/dqc_reference/reference_markers.hmm GCA_022783145.1_ASM2278314v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:24:52,752] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:24:52,753] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd1a8461b-2df4-4790-857d-6d48fe0a37d6/GCA_022783145.1_ASM2278314v1_genomic.fna.gz]
[2023-06-13 20:24:52,782] [INFO] Query marker FASTA was written to GCA_022783145.1_ASM2278314v1_genomic.fna/markers.fasta
[2023-06-13 20:24:52,782] [INFO] Task started: Blastn
[2023-06-13 20:24:52,782] [INFO] Running command: blastn -query GCA_022783145.1_ASM2278314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d94326b-2932-4f14-9029-6b3d3a5f6b15/dqc_reference/reference_markers.fasta -out GCA_022783145.1_ASM2278314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:24:53,314] [INFO] Task succeeded: Blastn
[2023-06-13 20:24:53,318] [INFO] Selected 15 target genomes.
[2023-06-13 20:24:53,318] [INFO] Target genome list was writen to GCA_022783145.1_ASM2278314v1_genomic.fna/target_genomes.txt
[2023-06-13 20:24:53,319] [INFO] Task started: fastANI
[2023-06-13 20:24:53,319] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1a8461b-2df4-4790-857d-6d48fe0a37d6/GCA_022783145.1_ASM2278314v1_genomic.fna.gz --refList GCA_022783145.1_ASM2278314v1_genomic.fna/target_genomes.txt --output GCA_022783145.1_ASM2278314v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:25:01,806] [INFO] Task succeeded: fastANI
[2023-06-13 20:25:01,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d94326b-2932-4f14-9029-6b3d3a5f6b15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:25:01,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d94326b-2932-4f14-9029-6b3d3a5f6b15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:25:01,814] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 20:25:01,814] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 20:25:01,814] [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
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	84.2168	536	920	95	below_threshold
Terrisporobacter petrolearius	strain=LAM0A37	GCA_020748185.1	1460447	1460447	type	True	83.7993	499	920	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	83.7247	511	920	95	below_threshold
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	83.6692	516	920	95	below_threshold
Terrisporobacter glycolicus	strain=ATCC 14880	GCA_000373865.1	36841	36841	suspected-type	True	83.6259	515	920	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	78.8112	243	920	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	78.3974	206	920	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	78.3852	210	920	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_000452245.2	1490	1490	type	True	78.3594	213	920	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	78.3168	218	920	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 20:25:01,815] [INFO] DFAST Taxonomy check result was written to GCA_022783145.1_ASM2278314v1_genomic.fna/tc_result.tsv
[2023-06-13 20:25:01,816] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:25:01,816] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:25:01,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d94326b-2932-4f14-9029-6b3d3a5f6b15/dqc_reference/checkm_data
[2023-06-13 20:25:01,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:25:01,854] [INFO] Task started: CheckM
[2023-06-13 20:25:01,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022783145.1_ASM2278314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022783145.1_ASM2278314v1_genomic.fna/checkm_input GCA_022783145.1_ASM2278314v1_genomic.fna/checkm_result
[2023-06-13 20:25:19,832] [INFO] Task succeeded: CheckM
[2023-06-13 20:25:19,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-13 20:25:19,850] [INFO] ===== Completeness check finished =====
[2023-06-13 20:25:19,851] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:25:19,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022783145.1_ASM2278314v1_genomic.fna/markers.fasta)
[2023-06-13 20:25:19,851] [INFO] Task started: Blastn
[2023-06-13 20:25:19,851] [INFO] Running command: blastn -query GCA_022783145.1_ASM2278314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d94326b-2932-4f14-9029-6b3d3a5f6b15/dqc_reference/reference_markers_gtdb.fasta -out GCA_022783145.1_ASM2278314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:25:20,557] [INFO] Task succeeded: Blastn
[2023-06-13 20:25:20,560] [INFO] Selected 16 target genomes.
[2023-06-13 20:25:20,561] [INFO] Target genome list was writen to GCA_022783145.1_ASM2278314v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:25:20,583] [INFO] Task started: fastANI
[2023-06-13 20:25:20,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1a8461b-2df4-4790-857d-6d48fe0a37d6/GCA_022783145.1_ASM2278314v1_genomic.fna.gz --refList GCA_022783145.1_ASM2278314v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022783145.1_ASM2278314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:25:28,438] [INFO] Task succeeded: fastANI
[2023-06-13 20:25:28,444] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 20:25:28,445] [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_900557165.1	s__Terrisporobacter sp900557165	85.0703	410	920	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.06	99.06	0.78	0.78	2	-
GCF_000808015.1	s__Terrisporobacter othiniensis	84.1994	537	920	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.48	99.45	0.91	0.90	3	-
GCA_902363255.1	s__Terrisporobacter sp902363255	84.1968	535	920	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000439105.1	s__Terrisporobacter glycolicus	83.7426	510	920	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.67	99.35	0.98	0.96	3	-
GCF_900114105.1	s__Terrisporobacter glycolicus_A	83.7186	503	920	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	98.29	98.07	0.91	0.91	3	-
GCF_014333445.1	s__Terrisporobacter mayombei	83.5322	250	920	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900002575.1	s__Romboutsia_C hominis	78.7757	245	920	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_C	95.0	98.29	95.25	0.93	0.90	6	-
GCF_006802875.1	s__Paraclostridium bifermentans	78.4044	209	920	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.64	96.79	0.90	0.86	14	-
GCF_000452245.2	s__Paraclostridium bifermentans_A	78.3594	213	920	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.39	96.64	0.88	0.81	7	-
GCF_017590215.1	s__CCUG-7971 sp017590215	78.1406	284	920	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__CCUG-7971	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 20:25:28,446] [INFO] GTDB search result was written to GCA_022783145.1_ASM2278314v1_genomic.fna/result_gtdb.tsv
[2023-06-13 20:25:28,447] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:25:28,449] [INFO] DFAST_QC result json was written to GCA_022783145.1_ASM2278314v1_genomic.fna/dqc_result.json
[2023-06-13 20:25:28,449] [INFO] DFAST_QC completed!
[2023-06-13 20:25:28,449] [INFO] Total running time: 0h0m41s