[2024-01-25 19:40:50,591] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:50,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:50,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg95cd8bf7-9ade-477a-9537-c2dc993ceb8c/dqc_reference
[2024-01-25 19:40:51,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:51,686] [INFO] Task started: Prodigal
[2024-01-25 19:40:51,686] [INFO] Running command: gunzip -c /var/lib/cwl/stga68b841f-2fd3-4641-8b39-47a78a69e0b6/GCF_014526325.1_ASM1452632v1_genomic.fna.gz | prodigal -d GCF_014526325.1_ASM1452632v1_genomic.fna/cds.fna -a GCF_014526325.1_ASM1452632v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:02,171] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:02,172] [INFO] Task started: HMMsearch
[2024-01-25 19:41:02,172] [INFO] Running command: hmmsearch --tblout GCF_014526325.1_ASM1452632v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95cd8bf7-9ade-477a-9537-c2dc993ceb8c/dqc_reference/reference_markers.hmm GCF_014526325.1_ASM1452632v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:02,394] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:02,395] [INFO] Found 6/6 markers.
[2024-01-25 19:41:02,427] [INFO] Query marker FASTA was written to GCF_014526325.1_ASM1452632v1_genomic.fna/markers.fasta
[2024-01-25 19:41:02,427] [INFO] Task started: Blastn
[2024-01-25 19:41:02,427] [INFO] Running command: blastn -query GCF_014526325.1_ASM1452632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95cd8bf7-9ade-477a-9537-c2dc993ceb8c/dqc_reference/reference_markers.fasta -out GCF_014526325.1_ASM1452632v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:03,083] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:03,089] [INFO] Selected 20 target genomes.
[2024-01-25 19:41:03,089] [INFO] Target genome list was writen to GCF_014526325.1_ASM1452632v1_genomic.fna/target_genomes.txt
[2024-01-25 19:41:03,104] [INFO] Task started: fastANI
[2024-01-25 19:41:03,104] [INFO] Running command: fastANI --query /var/lib/cwl/stga68b841f-2fd3-4641-8b39-47a78a69e0b6/GCF_014526325.1_ASM1452632v1_genomic.fna.gz --refList GCF_014526325.1_ASM1452632v1_genomic.fna/target_genomes.txt --output GCF_014526325.1_ASM1452632v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:41:16,497] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:16,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95cd8bf7-9ade-477a-9537-c2dc993ceb8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:41:16,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95cd8bf7-9ade-477a-9537-c2dc993ceb8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:41:16,510] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:41:16,510] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:41:16,510] [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
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	80.1472	642	1257	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	79.5702	510	1257	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	78.9425	489	1257	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.854	368	1257	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	77.9984	334	1257	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.9848	367	1257	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	77.9821	282	1257	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.9761	367	1257	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	77.9462	254	1257	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.8992	319	1257	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.7655	301	1257	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7342	216	1257	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.6696	263	1257	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.6551	259	1257	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.6336	261	1257	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	77.5974	223	1257	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	77.5175	263	1257	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.474	227	1257	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.4625	192	1257	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	77.2681	252	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:41:16,512] [INFO] DFAST Taxonomy check result was written to GCF_014526325.1_ASM1452632v1_genomic.fna/tc_result.tsv
[2024-01-25 19:41:16,513] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:41:16,513] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:41:16,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95cd8bf7-9ade-477a-9537-c2dc993ceb8c/dqc_reference/checkm_data
[2024-01-25 19:41:16,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:41:16,552] [INFO] Task started: CheckM
[2024-01-25 19:41:16,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014526325.1_ASM1452632v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014526325.1_ASM1452632v1_genomic.fna/checkm_input GCF_014526325.1_ASM1452632v1_genomic.fna/checkm_result
[2024-01-25 19:41:49,941] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:49,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:49,978] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:49,979] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:49,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014526325.1_ASM1452632v1_genomic.fna/markers.fasta)
[2024-01-25 19:41:49,979] [INFO] Task started: Blastn
[2024-01-25 19:41:49,979] [INFO] Running command: blastn -query GCF_014526325.1_ASM1452632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95cd8bf7-9ade-477a-9537-c2dc993ceb8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014526325.1_ASM1452632v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:50,940] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:50,946] [INFO] Selected 11 target genomes.
[2024-01-25 19:41:50,946] [INFO] Target genome list was writen to GCF_014526325.1_ASM1452632v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:50,955] [INFO] Task started: fastANI
[2024-01-25 19:41:50,955] [INFO] Running command: fastANI --query /var/lib/cwl/stga68b841f-2fd3-4641-8b39-47a78a69e0b6/GCF_014526325.1_ASM1452632v1_genomic.fna.gz --refList GCF_014526325.1_ASM1452632v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014526325.1_ASM1452632v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:59,630] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:59,638] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:59,638] [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_014526325.1	s__Psychroserpens algicola	100.0	1257	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002162685.1	s__Psychroserpens sp002162685	79.9835	611	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826645.1	s__Psychroserpens mesophilus	79.5866	509	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	79.5136	667	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104785.1	s__Psychroserpens sp900104785	79.4546	502	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	79.352	621	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479815.1	s__Psychroserpens sp905479815	79.1945	499	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799465.1	s__Psychroserpens sp000799465	79.1046	529	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222875.1	s__Psychroserpens sp018222875	79.0846	460	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	78.9702	538	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	78.9604	486	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:59,640] [INFO] GTDB search result was written to GCF_014526325.1_ASM1452632v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:59,640] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:59,644] [INFO] DFAST_QC result json was written to GCF_014526325.1_ASM1452632v1_genomic.fna/dqc_result.json
[2024-01-25 19:41:59,644] [INFO] DFAST_QC completed!
[2024-01-25 19:41:59,644] [INFO] Total running time: 0h1m9s