[2024-01-24 12:13:26,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:26,353] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:26,353] [INFO] DQC Reference Directory: /var/lib/cwl/stgb25facca-61d5-4409-9dba-9895caa40499/dqc_reference
[2024-01-24 12:13:27,606] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:27,607] [INFO] Task started: Prodigal
[2024-01-24 12:13:27,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ac397f1-dbaa-4599-9bb0-ec1c436fdfc8/GCF_900143685.1_PRJEB18025_genomic.fna.gz | prodigal -d GCF_900143685.1_PRJEB18025_genomic.fna/cds.fna -a GCF_900143685.1_PRJEB18025_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:34,518] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:34,519] [INFO] Task started: HMMsearch
[2024-01-24 12:13:34,519] [INFO] Running command: hmmsearch --tblout GCF_900143685.1_PRJEB18025_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb25facca-61d5-4409-9dba-9895caa40499/dqc_reference/reference_markers.hmm GCF_900143685.1_PRJEB18025_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:34,830] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:34,832] [INFO] Found 6/6 markers.
[2024-01-24 12:13:34,872] [INFO] Query marker FASTA was written to GCF_900143685.1_PRJEB18025_genomic.fna/markers.fasta
[2024-01-24 12:13:34,873] [INFO] Task started: Blastn
[2024-01-24 12:13:34,873] [INFO] Running command: blastn -query GCF_900143685.1_PRJEB18025_genomic.fna/markers.fasta -db /var/lib/cwl/stgb25facca-61d5-4409-9dba-9895caa40499/dqc_reference/reference_markers.fasta -out GCF_900143685.1_PRJEB18025_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:35,636] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:35,640] [INFO] Selected 16 target genomes.
[2024-01-24 12:13:35,641] [INFO] Target genome list was writen to GCF_900143685.1_PRJEB18025_genomic.fna/target_genomes.txt
[2024-01-24 12:13:35,696] [INFO] Task started: fastANI
[2024-01-24 12:13:35,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ac397f1-dbaa-4599-9bb0-ec1c436fdfc8/GCF_900143685.1_PRJEB18025_genomic.fna.gz --refList GCF_900143685.1_PRJEB18025_genomic.fna/target_genomes.txt --output GCF_900143685.1_PRJEB18025_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:43,480] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:43,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb25facca-61d5-4409-9dba-9895caa40499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:43,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb25facca-61d5-4409-9dba-9895caa40499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:43,491] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:43,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:43,492] [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
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	100.0	669	669	95	conclusive
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	89.1457	520	669	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	80.8195	285	669	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	80.089	271	669	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.5721	263	669	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.3238	209	669	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	79.301	238	669	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.2757	173	669	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.2092	208	669	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.1547	217	669	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	78.8802	176	669	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	78.8424	177	669	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:43,493] [INFO] DFAST Taxonomy check result was written to GCF_900143685.1_PRJEB18025_genomic.fna/tc_result.tsv
[2024-01-24 12:13:43,494] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:43,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:43,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb25facca-61d5-4409-9dba-9895caa40499/dqc_reference/checkm_data
[2024-01-24 12:13:43,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:43,522] [INFO] Task started: CheckM
[2024-01-24 12:13:43,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900143685.1_PRJEB18025_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900143685.1_PRJEB18025_genomic.fna/checkm_input GCF_900143685.1_PRJEB18025_genomic.fna/checkm_result
[2024-01-24 12:14:08,579] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:08,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:08,598] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:08,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:08,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900143685.1_PRJEB18025_genomic.fna/markers.fasta)
[2024-01-24 12:14:08,599] [INFO] Task started: Blastn
[2024-01-24 12:14:08,599] [INFO] Running command: blastn -query GCF_900143685.1_PRJEB18025_genomic.fna/markers.fasta -db /var/lib/cwl/stgb25facca-61d5-4409-9dba-9895caa40499/dqc_reference/reference_markers_gtdb.fasta -out GCF_900143685.1_PRJEB18025_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:09,778] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:09,782] [INFO] Selected 11 target genomes.
[2024-01-24 12:14:09,782] [INFO] Target genome list was writen to GCF_900143685.1_PRJEB18025_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:09,792] [INFO] Task started: fastANI
[2024-01-24 12:14:09,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ac397f1-dbaa-4599-9bb0-ec1c436fdfc8/GCF_900143685.1_PRJEB18025_genomic.fna.gz --refList GCF_900143685.1_PRJEB18025_genomic.fna/target_genomes_gtdb.txt --output GCF_900143685.1_PRJEB18025_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:14,980] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:14,991] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:14,992] [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_900143685.1	s__Parolsenella massiliensis	100.0	669	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	96.67	96.67	0.91	0.91	2	conclusive
GCF_003966955.1	s__Parolsenella catena	89.1746	523	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	98.03	97.75	0.95	0.92	5	-
GCA_900543875.1	s__Parolsenella sp900543875	86.4864	407	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	98.15	98.15	0.88	0.88	2	-
GCA_900544655.1	s__Parolsenella sp900544655	83.5105	286	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.93	99.93	0.89	0.89	2	-
GCA_900552935.1	s__Parolsenella sp900552935	83.2122	308	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901212675.1	s__Parolsenella uli_B	83.1025	388	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	96.31	96.31	0.90	0.90	2	-
GCA_900549525.1	s__Parolsenella sp900549525	82.3534	311	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.58	99.58	0.87	0.87	2	-
GCF_901212655.1	s__Parolsenella uli_A	81.7909	382	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540955.1	s__Paratractidigestivibacter sp900540955	80.5204	253	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.08	96.08	0.89	0.89	2	-
GCF_016899935.1	s__Thermophilibacter uli_B	80.3043	268	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544065.1	s__Collinsella sp900544065	78.8088	186	669	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:14,993] [INFO] GTDB search result was written to GCF_900143685.1_PRJEB18025_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:14,994] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:14,997] [INFO] DFAST_QC result json was written to GCF_900143685.1_PRJEB18025_genomic.fna/dqc_result.json
[2024-01-24 12:14:14,998] [INFO] DFAST_QC completed!
[2024-01-24 12:14:14,998] [INFO] Total running time: 0h0m49s