[2024-01-24 12:23:51,087] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:51,089] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:51,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg76ed2a8f-4918-43ce-b99d-4951f99b8a15/dqc_reference
[2024-01-24 12:23:52,356] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,357] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f18f325-251c-4276-b595-9665ad919706/GCF_013618625.1_ASM1361862v1_genomic.fna.gz | prodigal -d GCF_013618625.1_ASM1361862v1_genomic.fna/cds.fna -a GCF_013618625.1_ASM1361862v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:11,538] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:11,539] [INFO] Task started: HMMsearch
[2024-01-24 12:24:11,539] [INFO] Running command: hmmsearch --tblout GCF_013618625.1_ASM1361862v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76ed2a8f-4918-43ce-b99d-4951f99b8a15/dqc_reference/reference_markers.hmm GCF_013618625.1_ASM1361862v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:11,840] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:11,842] [INFO] Found 6/6 markers.
[2024-01-24 12:24:11,900] [INFO] Query marker FASTA was written to GCF_013618625.1_ASM1361862v1_genomic.fna/markers.fasta
[2024-01-24 12:24:11,901] [INFO] Task started: Blastn
[2024-01-24 12:24:11,901] [INFO] Running command: blastn -query GCF_013618625.1_ASM1361862v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76ed2a8f-4918-43ce-b99d-4951f99b8a15/dqc_reference/reference_markers.fasta -out GCF_013618625.1_ASM1361862v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:12,477] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:12,481] [INFO] Selected 13 target genomes.
[2024-01-24 12:24:12,481] [INFO] Target genome list was writen to GCF_013618625.1_ASM1361862v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:12,487] [INFO] Task started: fastANI
[2024-01-24 12:24:12,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f18f325-251c-4276-b595-9665ad919706/GCF_013618625.1_ASM1361862v1_genomic.fna.gz --refList GCF_013618625.1_ASM1361862v1_genomic.fna/target_genomes.txt --output GCF_013618625.1_ASM1361862v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:27,912] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:27,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76ed2a8f-4918-43ce-b99d-4951f99b8a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:27,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76ed2a8f-4918-43ce-b99d-4951f99b8a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:27,923] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:27,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:27,924] [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
Bremerella alba	strain=FF15	GCA_013618625.1	980252	980252	type	True	100.0	2107	2111	95	conclusive
Bremerella volcania	strain=Pan97	GCA_007748115.1	2527984	2527984	type	True	82.9741	1495	2111	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	76.6532	183	2111	95	below_threshold
Blastopirellula marina	strain=DSM 3645	GCA_000153105.1	124	124	suspected-type	True	76.6266	173	2111	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.9835	51	2111	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.7487	58	2111	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:27,925] [INFO] DFAST Taxonomy check result was written to GCF_013618625.1_ASM1361862v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:27,926] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:27,926] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:27,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76ed2a8f-4918-43ce-b99d-4951f99b8a15/dqc_reference/checkm_data
[2024-01-24 12:24:27,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:27,985] [INFO] Task started: CheckM
[2024-01-24 12:24:27,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013618625.1_ASM1361862v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013618625.1_ASM1361862v1_genomic.fna/checkm_input GCF_013618625.1_ASM1361862v1_genomic.fna/checkm_result
[2024-01-24 12:25:24,628] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:24,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:24,652] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:24,653] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:24,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013618625.1_ASM1361862v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:24,653] [INFO] Task started: Blastn
[2024-01-24 12:25:24,654] [INFO] Running command: blastn -query GCF_013618625.1_ASM1361862v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76ed2a8f-4918-43ce-b99d-4951f99b8a15/dqc_reference/reference_markers_gtdb.fasta -out GCF_013618625.1_ASM1361862v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:25,430] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:25,434] [INFO] Selected 6 target genomes.
[2024-01-24 12:25:25,435] [INFO] Target genome list was writen to GCF_013618625.1_ASM1361862v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:25,440] [INFO] Task started: fastANI
[2024-01-24 12:25:25,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f18f325-251c-4276-b595-9665ad919706/GCF_013618625.1_ASM1361862v1_genomic.fna.gz --refList GCF_013618625.1_ASM1361862v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013618625.1_ASM1361862v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:34,567] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:34,579] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:34,580] [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_013618625.1	s__Bremerella alba	100.0	2107	2111	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007748115.1	s__Bremerella volcania	82.989	1493	2111	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002967715.1	s__Bremerella marina_B	82.3907	1437	2111	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016124445.1	s__Bremerella sp016124445	78.4577	479	2111	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335505.1	s__Bremerella cremea_A	78.2875	641	2111	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002967765.1	s__Bremerella marina_A	78.2719	632	2111	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:34,582] [INFO] GTDB search result was written to GCF_013618625.1_ASM1361862v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:34,582] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:34,587] [INFO] DFAST_QC result json was written to GCF_013618625.1_ASM1361862v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:34,587] [INFO] DFAST_QC completed!
[2024-01-24 12:25:34,587] [INFO] Total running time: 0h1m44s