[2023-06-27 11:44:30,089] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:44:30,093] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:44:30,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg2db0f234-9be1-496b-94c8-893140837e91/dqc_reference
[2023-06-27 11:44:34,010] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:44:34,013] [INFO] Task started: Prodigal
[2023-06-27 11:44:34,014] [INFO] Running command: gunzip -c /var/lib/cwl/stgeeaa89d3-2d31-4352-a68c-81134e863008/GCA_026421165.1_ASM2642116v1_genomic.fna.gz | prodigal -d GCA_026421165.1_ASM2642116v1_genomic.fna/cds.fna -a GCA_026421165.1_ASM2642116v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:44:53,847] [INFO] Task succeeded: Prodigal
[2023-06-27 11:44:53,848] [INFO] Task started: HMMsearch
[2023-06-27 11:44:53,848] [INFO] Running command: hmmsearch --tblout GCA_026421165.1_ASM2642116v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2db0f234-9be1-496b-94c8-893140837e91/dqc_reference/reference_markers.hmm GCA_026421165.1_ASM2642116v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:44:54,175] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:44:54,177] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeeaa89d3-2d31-4352-a68c-81134e863008/GCA_026421165.1_ASM2642116v1_genomic.fna.gz]
[2023-06-27 11:44:54,221] [INFO] Query marker FASTA was written to GCA_026421165.1_ASM2642116v1_genomic.fna/markers.fasta
[2023-06-27 11:44:54,222] [INFO] Task started: Blastn
[2023-06-27 11:44:54,222] [INFO] Running command: blastn -query GCA_026421165.1_ASM2642116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db0f234-9be1-496b-94c8-893140837e91/dqc_reference/reference_markers.fasta -out GCA_026421165.1_ASM2642116v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:44:54,861] [INFO] Task succeeded: Blastn
[2023-06-27 11:44:54,894] [INFO] Selected 12 target genomes.
[2023-06-27 11:44:54,894] [INFO] Target genome list was writen to GCA_026421165.1_ASM2642116v1_genomic.fna/target_genomes.txt
[2023-06-27 11:44:54,897] [INFO] Task started: fastANI
[2023-06-27 11:44:54,897] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeaa89d3-2d31-4352-a68c-81134e863008/GCA_026421165.1_ASM2642116v1_genomic.fna.gz --refList GCA_026421165.1_ASM2642116v1_genomic.fna/target_genomes.txt --output GCA_026421165.1_ASM2642116v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:45:06,607] [INFO] Task succeeded: fastANI
[2023-06-27 11:45:06,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2db0f234-9be1-496b-94c8-893140837e91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:45:06,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2db0f234-9be1-496b-94c8-893140837e91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:45:06,623] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:45:06,623] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:45:06,623] [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
Neolewinella aurantiaca	strain=SSH13	GCA_008014675.1	2602767	2602767	type	True	78.7041	586	1252	95	below_threshold
Neolewinella persica	strain=DSM 23188	GCA_000373105.1	70998	70998	type	True	77.4514	321	1252	95	below_threshold
Neolewinella agarilytica	strain=DSM 24740	GCA_900110645.1	478744	478744	type	True	77.1372	246	1252	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	76.8562	146	1252	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	76.782	150	1252	95	below_threshold
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	76.7411	238	1252	95	below_threshold
Neolewinella antarctica	strain=DSM 105096	GCA_011927835.1	442734	442734	type	True	76.5707	165	1252	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	76.4343	119	1252	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	76.3332	130	1252	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:45:06,625] [INFO] DFAST Taxonomy check result was written to GCA_026421165.1_ASM2642116v1_genomic.fna/tc_result.tsv
[2023-06-27 11:45:06,626] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:45:06,626] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:45:06,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2db0f234-9be1-496b-94c8-893140837e91/dqc_reference/checkm_data
[2023-06-27 11:45:06,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:45:06,678] [INFO] Task started: CheckM
[2023-06-27 11:45:06,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026421165.1_ASM2642116v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026421165.1_ASM2642116v1_genomic.fna/checkm_input GCA_026421165.1_ASM2642116v1_genomic.fna/checkm_result
[2023-06-27 11:46:03,448] [INFO] Task succeeded: CheckM
[2023-06-27 11:46:03,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:46:03,478] [INFO] ===== Completeness check finished =====
[2023-06-27 11:46:03,478] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:46:03,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026421165.1_ASM2642116v1_genomic.fna/markers.fasta)
[2023-06-27 11:46:03,480] [INFO] Task started: Blastn
[2023-06-27 11:46:03,480] [INFO] Running command: blastn -query GCA_026421165.1_ASM2642116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db0f234-9be1-496b-94c8-893140837e91/dqc_reference/reference_markers_gtdb.fasta -out GCA_026421165.1_ASM2642116v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:46:04,361] [INFO] Task succeeded: Blastn
[2023-06-27 11:46:04,368] [INFO] Selected 16 target genomes.
[2023-06-27 11:46:04,369] [INFO] Target genome list was writen to GCA_026421165.1_ASM2642116v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:46:04,403] [INFO] Task started: fastANI
[2023-06-27 11:46:04,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeaa89d3-2d31-4352-a68c-81134e863008/GCA_026421165.1_ASM2642116v1_genomic.fna.gz --refList GCA_026421165.1_ASM2642116v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026421165.1_ASM2642116v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:46:21,872] [INFO] Task succeeded: fastANI
[2023-06-27 11:46:21,886] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:46:21,887] [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_008014675.1	s__Lewinella_A aurantiaca	78.7153	584	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373105.1	s__Lewinella_A persica	77.4586	320	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110645.1	s__Lewinella_A agarilytica	77.1593	244	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	76.8562	146	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001625015.1	s__Lewinella_A sp001625015	76.8334	160	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349155.1	s__Lewinella_A lacunae	76.7411	238	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927835.1	s__Lewinella_A antarctica	76.5838	164	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197245.1	s__Lewinella_A aquimaris	76.4343	119	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390935.1	s__Lewinella_A sp003390935	76.4335	125	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004375085.3	s__Lewinella_A sp004375085	76.4196	157	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390915.1	s__Lewinella_A sp003390915	76.3853	153	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002591745.1	s__Lewinella_A sp002591745	76.345	67	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803465.1	s__Lewinella_A litorea	76.3332	130	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:46:21,889] [INFO] GTDB search result was written to GCA_026421165.1_ASM2642116v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:46:21,889] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:46:21,894] [INFO] DFAST_QC result json was written to GCA_026421165.1_ASM2642116v1_genomic.fna/dqc_result.json
[2023-06-27 11:46:21,895] [INFO] DFAST_QC completed!
[2023-06-27 11:46:21,895] [INFO] Total running time: 0h1m52s