[2023-06-30 20:51:02,076] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:51:02,078] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:51:02,078] [INFO] DQC Reference Directory: /var/lib/cwl/stg625b966d-48f9-4612-97a6-bb3b651f58b9/dqc_reference
[2023-06-30 20:51:03,273] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:51:03,274] [INFO] Task started: Prodigal
[2023-06-30 20:51:03,274] [INFO] Running command: gunzip -c /var/lib/cwl/stga8b2be90-3d77-4440-9b19-30135ee9ae90/GCA_016715405.1_ASM1671540v1_genomic.fna.gz | prodigal -d GCA_016715405.1_ASM1671540v1_genomic.fna/cds.fna -a GCA_016715405.1_ASM1671540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:51:35,299] [INFO] Task succeeded: Prodigal
[2023-06-30 20:51:35,299] [INFO] Task started: HMMsearch
[2023-06-30 20:51:35,299] [INFO] Running command: hmmsearch --tblout GCA_016715405.1_ASM1671540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg625b966d-48f9-4612-97a6-bb3b651f58b9/dqc_reference/reference_markers.hmm GCA_016715405.1_ASM1671540v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:51:35,602] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:51:35,603] [INFO] Found 6/6 markers.
[2023-06-30 20:51:35,653] [INFO] Query marker FASTA was written to GCA_016715405.1_ASM1671540v1_genomic.fna/markers.fasta
[2023-06-30 20:51:35,653] [INFO] Task started: Blastn
[2023-06-30 20:51:35,653] [INFO] Running command: blastn -query GCA_016715405.1_ASM1671540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg625b966d-48f9-4612-97a6-bb3b651f58b9/dqc_reference/reference_markers.fasta -out GCA_016715405.1_ASM1671540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:51:36,243] [INFO] Task succeeded: Blastn
[2023-06-30 20:51:36,248] [INFO] Selected 32 target genomes.
[2023-06-30 20:51:36,248] [INFO] Target genome list was writen to GCA_016715405.1_ASM1671540v1_genomic.fna/target_genomes.txt
[2023-06-30 20:51:36,251] [INFO] Task started: fastANI
[2023-06-30 20:51:36,252] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b2be90-3d77-4440-9b19-30135ee9ae90/GCA_016715405.1_ASM1671540v1_genomic.fna.gz --refList GCA_016715405.1_ASM1671540v1_genomic.fna/target_genomes.txt --output GCA_016715405.1_ASM1671540v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:51:59,237] [INFO] Task succeeded: fastANI
[2023-06-30 20:51:59,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg625b966d-48f9-4612-97a6-bb3b651f58b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:51:59,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg625b966d-48f9-4612-97a6-bb3b651f58b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:51:59,247] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:51:59,247] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:51:59,247] [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 marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	76.1999	53	1952	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	75.9013	52	1952	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	75.4047	50	1952	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:51:59,249] [INFO] DFAST Taxonomy check result was written to GCA_016715405.1_ASM1671540v1_genomic.fna/tc_result.tsv
[2023-06-30 20:51:59,250] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:51:59,250] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:51:59,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg625b966d-48f9-4612-97a6-bb3b651f58b9/dqc_reference/checkm_data
[2023-06-30 20:51:59,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:51:59,314] [INFO] Task started: CheckM
[2023-06-30 20:51:59,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016715405.1_ASM1671540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016715405.1_ASM1671540v1_genomic.fna/checkm_input GCA_016715405.1_ASM1671540v1_genomic.fna/checkm_result
[2023-06-30 20:53:22,884] [INFO] Task succeeded: CheckM
[2023-06-30 20:53:22,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:53:22,909] [INFO] ===== Completeness check finished =====
[2023-06-30 20:53:22,910] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:53:22,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016715405.1_ASM1671540v1_genomic.fna/markers.fasta)
[2023-06-30 20:53:22,910] [INFO] Task started: Blastn
[2023-06-30 20:53:22,911] [INFO] Running command: blastn -query GCA_016715405.1_ASM1671540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg625b966d-48f9-4612-97a6-bb3b651f58b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_016715405.1_ASM1671540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:53:23,694] [INFO] Task succeeded: Blastn
[2023-06-30 20:53:23,699] [INFO] Selected 17 target genomes.
[2023-06-30 20:53:23,699] [INFO] Target genome list was writen to GCA_016715405.1_ASM1671540v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:53:23,706] [INFO] Task started: fastANI
[2023-06-30 20:53:23,707] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b2be90-3d77-4440-9b19-30135ee9ae90/GCA_016715405.1_ASM1671540v1_genomic.fna.gz --refList GCA_016715405.1_ASM1671540v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016715405.1_ASM1671540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:53:40,263] [INFO] Task succeeded: fastANI
[2023-06-30 20:53:40,278] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:53:40,278] [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_016715405.1	s__JABWBR01 sp016715405	100.0	1950	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013360405.1	s__JABWBR01 sp013360405	90.8106	1472	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787505.1	s__JABWBR01 sp016787505	90.7747	1060	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711045.1	s__JADJTT01 sp016711045	76.8102	74	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJTT01	95.0	99.22	99.22	0.93	0.93	2	-
GCA_016703765.1	s__JADJTT01 sp016703765	76.6376	116	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJTT01	95.0	98.25	98.24	0.94	0.92	3	-
GCA_016719605.1	s__M3007 sp016719605	76.4525	82	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908745.1	s__Phaeodactylibacter sp009908745	76.094	65	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787345.1	s__M3007 sp016787345	75.9634	91	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490175.1	s__WFYJ01 sp015490175	75.9259	80	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__WFYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361075.1	s__JABWAJ01 sp013361075	75.7832	84	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWAJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013299105.1	s__Haliscomenobacter sp013299105	75.641	63	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Haliscomenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321935.1	s__UBA6168 sp011321935	75.5039	51	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA6168	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:53:40,280] [INFO] GTDB search result was written to GCA_016715405.1_ASM1671540v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:53:40,281] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:53:40,284] [INFO] DFAST_QC result json was written to GCA_016715405.1_ASM1671540v1_genomic.fna/dqc_result.json
[2023-06-30 20:53:40,284] [INFO] DFAST_QC completed!
[2023-06-30 20:53:40,284] [INFO] Total running time: 0h2m38s