[2023-06-04 23:12:03,951] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:12:03,954] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:12:03,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e844bc7-4e0b-4408-a567-a14bd59618c7/dqc_reference
[2023-06-04 23:12:05,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:12:05,870] [INFO] Task started: Prodigal
[2023-06-04 23:12:05,871] [INFO] Running command: gunzip -c /var/lib/cwl/stgb636e97a-8316-432c-b009-b229e8837008/GCA_004556545.1_ASM455654v1_genomic.fna.gz | prodigal -d GCA_004556545.1_ASM455654v1_genomic.fna/cds.fna -a GCA_004556545.1_ASM455654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:12:14,363] [INFO] Task succeeded: Prodigal
[2023-06-04 23:12:14,363] [INFO] Task started: HMMsearch
[2023-06-04 23:12:14,363] [INFO] Running command: hmmsearch --tblout GCA_004556545.1_ASM455654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e844bc7-4e0b-4408-a567-a14bd59618c7/dqc_reference/reference_markers.hmm GCA_004556545.1_ASM455654v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:12:14,672] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:12:14,674] [INFO] Found 6/6 markers.
[2023-06-04 23:12:14,718] [INFO] Query marker FASTA was written to GCA_004556545.1_ASM455654v1_genomic.fna/markers.fasta
[2023-06-04 23:12:14,719] [INFO] Task started: Blastn
[2023-06-04 23:12:14,719] [INFO] Running command: blastn -query GCA_004556545.1_ASM455654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e844bc7-4e0b-4408-a567-a14bd59618c7/dqc_reference/reference_markers.fasta -out GCA_004556545.1_ASM455654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:12:15,348] [INFO] Task succeeded: Blastn
[2023-06-04 23:12:15,352] [INFO] Selected 31 target genomes.
[2023-06-04 23:12:15,352] [INFO] Target genome list was writen to GCA_004556545.1_ASM455654v1_genomic.fna/target_genomes.txt
[2023-06-04 23:12:15,414] [INFO] Task started: fastANI
[2023-06-04 23:12:15,414] [INFO] Running command: fastANI --query /var/lib/cwl/stgb636e97a-8316-432c-b009-b229e8837008/GCA_004556545.1_ASM455654v1_genomic.fna.gz --refList GCA_004556545.1_ASM455654v1_genomic.fna/target_genomes.txt --output GCA_004556545.1_ASM455654v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:12:34,744] [INFO] Task succeeded: fastANI
[2023-06-04 23:12:34,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e844bc7-4e0b-4408-a567-a14bd59618c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:12:34,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e844bc7-4e0b-4408-a567-a14bd59618c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:12:34,748] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:12:34,748] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 23:12:34,748] [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
--------------------------------------------------------------------------------
[2023-06-04 23:12:34,750] [INFO] DFAST Taxonomy check result was written to GCA_004556545.1_ASM455654v1_genomic.fna/tc_result.tsv
[2023-06-04 23:12:34,751] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:12:34,751] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:12:34,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e844bc7-4e0b-4408-a567-a14bd59618c7/dqc_reference/checkm_data
[2023-06-04 23:12:34,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:12:34,791] [INFO] Task started: CheckM
[2023-06-04 23:12:34,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004556545.1_ASM455654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004556545.1_ASM455654v1_genomic.fna/checkm_input GCA_004556545.1_ASM455654v1_genomic.fna/checkm_result
[2023-06-04 23:13:04,467] [INFO] Task succeeded: CheckM
[2023-06-04 23:13:04,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:13:04,493] [INFO] ===== Completeness check finished =====
[2023-06-04 23:13:04,494] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:13:04,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004556545.1_ASM455654v1_genomic.fna/markers.fasta)
[2023-06-04 23:13:04,494] [INFO] Task started: Blastn
[2023-06-04 23:13:04,495] [INFO] Running command: blastn -query GCA_004556545.1_ASM455654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e844bc7-4e0b-4408-a567-a14bd59618c7/dqc_reference/reference_markers_gtdb.fasta -out GCA_004556545.1_ASM455654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:13:05,433] [INFO] Task succeeded: Blastn
[2023-06-04 23:13:05,438] [INFO] Selected 12 target genomes.
[2023-06-04 23:13:05,438] [INFO] Target genome list was writen to GCA_004556545.1_ASM455654v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:13:05,542] [INFO] Task started: fastANI
[2023-06-04 23:13:05,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgb636e97a-8316-432c-b009-b229e8837008/GCA_004556545.1_ASM455654v1_genomic.fna.gz --refList GCA_004556545.1_ASM455654v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004556545.1_ASM455654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:13:13,910] [INFO] Task succeeded: fastANI
[2023-06-04 23:13:13,925] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:13:13,926] [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_004556545.1	s__Limiplasma sp004556545	100.0	978	987	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	98.65	98.59	0.84	0.84	3	conclusive
GCA_900548145.1	s__Limiplasma sp900548145	88.9761	620	987	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	98.68	97.90	0.90	0.87	4	-
GCA_017937655.1	s__Limiplasma sp017937655	79.781	298	987	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056145.1	s__Limiplasma sp015056145	78.765	241	987	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540045.1	s__Limiplasma merdipullorum	78.7033	261	987	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	97.42	97.19	0.80	0.74	6	-
GCA_017516765.1	s__Limiplasma sp017516765	78.4389	215	987	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056315.1	s__Limiplasma sp015056315	78.3828	229	987	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938645.1	s__Limiplasma sp017938645	78.2055	206	987	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550955.1	s__Limiplasma sp900550955	78.1536	190	987	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015056365.1	s__Limiplasma sp015056365	78.1218	212	987	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:13:13,927] [INFO] GTDB search result was written to GCA_004556545.1_ASM455654v1_genomic.fna/result_gtdb.tsv
[2023-06-04 23:13:13,928] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:13:13,931] [INFO] DFAST_QC result json was written to GCA_004556545.1_ASM455654v1_genomic.fna/dqc_result.json
[2023-06-04 23:13:13,931] [INFO] DFAST_QC completed!
[2023-06-04 23:13:13,931] [INFO] Total running time: 0h1m10s