[2023-06-29 14:37:25,683] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:37:25,685] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:37:25,686] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdedf915-d062-4d3c-9b81-99d9d933bfdc/dqc_reference
[2023-06-29 14:37:27,085] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:37:27,086] [INFO] Task started: Prodigal
[2023-06-29 14:37:27,086] [INFO] Running command: gunzip -c /var/lib/cwl/stge51d5333-a750-4589-8868-cb6d89afc18e/GCA_023708345.1_ASM2370834v1_genomic.fna.gz | prodigal -d GCA_023708345.1_ASM2370834v1_genomic.fna/cds.fna -a GCA_023708345.1_ASM2370834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:37:34,242] [INFO] Task succeeded: Prodigal
[2023-06-29 14:37:34,243] [INFO] Task started: HMMsearch
[2023-06-29 14:37:34,243] [INFO] Running command: hmmsearch --tblout GCA_023708345.1_ASM2370834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdedf915-d062-4d3c-9b81-99d9d933bfdc/dqc_reference/reference_markers.hmm GCA_023708345.1_ASM2370834v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:37:34,513] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:37:34,514] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge51d5333-a750-4589-8868-cb6d89afc18e/GCA_023708345.1_ASM2370834v1_genomic.fna.gz]
[2023-06-29 14:37:34,539] [INFO] Query marker FASTA was written to GCA_023708345.1_ASM2370834v1_genomic.fna/markers.fasta
[2023-06-29 14:37:34,539] [INFO] Task started: Blastn
[2023-06-29 14:37:34,539] [INFO] Running command: blastn -query GCA_023708345.1_ASM2370834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdedf915-d062-4d3c-9b81-99d9d933bfdc/dqc_reference/reference_markers.fasta -out GCA_023708345.1_ASM2370834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:37:35,252] [INFO] Task succeeded: Blastn
[2023-06-29 14:37:35,256] [INFO] Selected 7 target genomes.
[2023-06-29 14:37:35,257] [INFO] Target genome list was writen to GCA_023708345.1_ASM2370834v1_genomic.fna/target_genomes.txt
[2023-06-29 14:37:35,258] [INFO] Task started: fastANI
[2023-06-29 14:37:35,258] [INFO] Running command: fastANI --query /var/lib/cwl/stge51d5333-a750-4589-8868-cb6d89afc18e/GCA_023708345.1_ASM2370834v1_genomic.fna.gz --refList GCA_023708345.1_ASM2370834v1_genomic.fna/target_genomes.txt --output GCA_023708345.1_ASM2370834v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:37:40,160] [INFO] Task succeeded: fastANI
[2023-06-29 14:37:40,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdedf915-d062-4d3c-9b81-99d9d933bfdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:37:40,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdedf915-d062-4d3c-9b81-99d9d933bfdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:37:40,183] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:37:40,183] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:37:40,183] [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
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	85.62	571	804	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	84.8298	553	804	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	84.7953	561	804	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	84.2083	541	804	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	81.6946	357	804	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.9823	181	804	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.0023	190	804	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:37:40,186] [INFO] DFAST Taxonomy check result was written to GCA_023708345.1_ASM2370834v1_genomic.fna/tc_result.tsv
[2023-06-29 14:37:40,186] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:37:40,187] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:37:40,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdedf915-d062-4d3c-9b81-99d9d933bfdc/dqc_reference/checkm_data
[2023-06-29 14:37:40,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:37:40,225] [INFO] Task started: CheckM
[2023-06-29 14:37:40,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708345.1_ASM2370834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708345.1_ASM2370834v1_genomic.fna/checkm_input GCA_023708345.1_ASM2370834v1_genomic.fna/checkm_result
[2023-06-29 14:38:06,795] [INFO] Task succeeded: CheckM
[2023-06-29 14:38:06,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:38:06,828] [INFO] ===== Completeness check finished =====
[2023-06-29 14:38:06,829] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:38:06,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708345.1_ASM2370834v1_genomic.fna/markers.fasta)
[2023-06-29 14:38:06,830] [INFO] Task started: Blastn
[2023-06-29 14:38:06,830] [INFO] Running command: blastn -query GCA_023708345.1_ASM2370834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdedf915-d062-4d3c-9b81-99d9d933bfdc/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708345.1_ASM2370834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:38:08,039] [INFO] Task succeeded: Blastn
[2023-06-29 14:38:08,043] [INFO] Selected 12 target genomes.
[2023-06-29 14:38:08,044] [INFO] Target genome list was writen to GCA_023708345.1_ASM2370834v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:38:08,048] [INFO] Task started: fastANI
[2023-06-29 14:38:08,048] [INFO] Running command: fastANI --query /var/lib/cwl/stge51d5333-a750-4589-8868-cb6d89afc18e/GCA_023708345.1_ASM2370834v1_genomic.fna.gz --refList GCA_023708345.1_ASM2370834v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708345.1_ASM2370834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:38:15,829] [INFO] Task succeeded: fastANI
[2023-06-29 14:38:15,843] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:38:15,843] [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_003293635.1	s__Faecalibacterium prausnitzii_G	96.3056	666	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.11	95.97	0.86	0.76	34	conclusive
GCA_900758465.1	s__Faecalibacterium sp900758465	91.3222	569	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.14	97.85	0.88	0.87	4	-
GCA_002313795.1	s__Faecalibacterium prausnitzii_L	86.4587	407	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.80	98.80	0.73	0.73	2	-
GCF_002549975.1	s__Faecalibacterium prausnitzii_H	85.7325	582	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.03	97.77	0.90	0.86	9	-
GCF_002550035.1	s__Faecalibacterium prausnitzii_E	85.6372	563	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.41	96.74	0.87	0.80	12	-
GCF_002549775.1	s__Faecalibacterium prausnitzii_F	84.8513	551	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.99	97.71	0.95	0.94	3	-
GCF_003287495.1	s__Faecalibacterium prausnitzii_I	84.824	563	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.17	97.28	0.90	0.84	9	-
GCA_900539945.1	s__Faecalibacterium sp900539945	84.738	506	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.71	98.00	0.92	0.86	4	-
GCA_014858325.1	s__Faecalibacterium sp014858325	84.5112	368	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287405.1	s__Faecalibacterium prausnitzii_J	84.4707	540	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.32	96.98	0.87	0.83	5	-
GCF_003324185.1	s__Faecalibacterium prausnitzii	84.2225	540	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.64	96.12	0.86	0.79	47	-
GCA_905215595.1	s__Faecalibacterium sp905215595	82.3742	382	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:38:15,845] [INFO] GTDB search result was written to GCA_023708345.1_ASM2370834v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:38:15,846] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:38:15,852] [INFO] DFAST_QC result json was written to GCA_023708345.1_ASM2370834v1_genomic.fna/dqc_result.json
[2023-06-29 14:38:15,852] [INFO] DFAST_QC completed!
[2023-06-29 14:38:15,852] [INFO] Total running time: 0h0m50s