[2024-01-24 10:48:09,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,565] [INFO] DQC Reference Directory: /var/lib/cwl/stged22004c-b052-4e65-8a45-5f1fc21f4ae7/dqc_reference
[2024-01-24 10:48:23,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,956] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a132596-9c17-4356-b855-bdced8a5f89d/GCF_002000085.1_ASM200008v1_genomic.fna.gz | prodigal -d GCF_002000085.1_ASM200008v1_genomic.fna/cds.fna -a GCF_002000085.1_ASM200008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:32,091] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:32,091] [INFO] Task started: HMMsearch
[2024-01-24 10:48:32,092] [INFO] Running command: hmmsearch --tblout GCF_002000085.1_ASM200008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged22004c-b052-4e65-8a45-5f1fc21f4ae7/dqc_reference/reference_markers.hmm GCF_002000085.1_ASM200008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:32,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:32,408] [INFO] Found 6/6 markers.
[2024-01-24 10:48:32,466] [INFO] Query marker FASTA was written to GCF_002000085.1_ASM200008v1_genomic.fna/markers.fasta
[2024-01-24 10:48:32,466] [INFO] Task started: Blastn
[2024-01-24 10:48:32,466] [INFO] Running command: blastn -query GCF_002000085.1_ASM200008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged22004c-b052-4e65-8a45-5f1fc21f4ae7/dqc_reference/reference_markers.fasta -out GCF_002000085.1_ASM200008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:33,175] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:33,179] [INFO] Selected 19 target genomes.
[2024-01-24 10:48:33,180] [INFO] Target genome list was writen to GCF_002000085.1_ASM200008v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:33,188] [INFO] Task started: fastANI
[2024-01-24 10:48:33,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a132596-9c17-4356-b855-bdced8a5f89d/GCF_002000085.1_ASM200008v1_genomic.fna.gz --refList GCF_002000085.1_ASM200008v1_genomic.fna/target_genomes.txt --output GCF_002000085.1_ASM200008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:47,016] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:47,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged22004c-b052-4e65-8a45-5f1fc21f4ae7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:47,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged22004c-b052-4e65-8a45-5f1fc21f4ae7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:47,037] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:47,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:47,037] [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
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	100.0	1548	1550	95	conclusive
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.4724	239	1550	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.2131	231	1550	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.1651	256	1550	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.1626	217	1550	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.091	212	1550	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.0078	200	1550	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	78.0003	249	1550	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.9751	255	1550	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.9122	271	1550	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.4226	179	1550	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.3627	90	1550	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	76.2674	114	1550	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	75.9606	73	1550	95	below_threshold
Pseudoalteromonas piratica	strain=OCN003	GCA_000788395.1	1348114	1348114	type	True	75.932	55	1550	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:47,039] [INFO] DFAST Taxonomy check result was written to GCF_002000085.1_ASM200008v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:47,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:47,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:47,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged22004c-b052-4e65-8a45-5f1fc21f4ae7/dqc_reference/checkm_data
[2024-01-24 10:48:47,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:47,088] [INFO] Task started: CheckM
[2024-01-24 10:48:47,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002000085.1_ASM200008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002000085.1_ASM200008v1_genomic.fna/checkm_input GCF_002000085.1_ASM200008v1_genomic.fna/checkm_result
[2024-01-24 10:49:20,034] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:20,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:20,132] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:20,132] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:20,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002000085.1_ASM200008v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:20,133] [INFO] Task started: Blastn
[2024-01-24 10:49:20,133] [INFO] Running command: blastn -query GCF_002000085.1_ASM200008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged22004c-b052-4e65-8a45-5f1fc21f4ae7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002000085.1_ASM200008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:21,913] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:21,916] [INFO] Selected 23 target genomes.
[2024-01-24 10:49:21,916] [INFO] Target genome list was writen to GCF_002000085.1_ASM200008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:21,931] [INFO] Task started: fastANI
[2024-01-24 10:49:21,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a132596-9c17-4356-b855-bdced8a5f89d/GCF_002000085.1_ASM200008v1_genomic.fna.gz --refList GCF_002000085.1_ASM200008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002000085.1_ASM200008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:42,070] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:42,086] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:42,087] [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_002000085.1	s__Pseudocolwellia agarivorans	100.0	1548	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudocolwellia	95.0	95.36	95.36	0.90	0.90	2	conclusive
GCF_018860755.1	s__Colwellia sp018860755	78.457	225	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	78.4424	316	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	78.4127	284	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	78.3887	298	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	78.3765	270	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002104515.1	s__Cognaticolwellia polaris	78.2566	296	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215295.1	s__Colwellia_A sp013215295	78.2173	239	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207645.1	s__Thalassotalea_B piscium	78.1428	217	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439335.1	s__Litorilituus lipolyticus	78.0911	212	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	78.0824	232	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_018860585.1	s__Colwellia sp018860585	78.0674	242	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836255.1	s__Colwellia sp002836255	78.0551	233	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491935.1	s__GCA-2401725 sp015491935	78.0108	196	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954275.1	s__Colwellia demingiae	78.0047	252	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653195.1	s__Thalassotalea_B profundi	78.0003	249	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295665.1	s__Litorilituus sediminis	77.9832	216	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215655.1	s__Colwellia_A sp013215655	77.9688	296	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	77.7578	250	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	76.3825	99	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005886875.1	s__Pseudoalteromonas aurantia_A	76.2754	55	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.47	99.41	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:42,089] [INFO] GTDB search result was written to GCF_002000085.1_ASM200008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:42,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:42,093] [INFO] DFAST_QC result json was written to GCF_002000085.1_ASM200008v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:42,094] [INFO] DFAST_QC completed!
[2024-01-24 10:49:42,094] [INFO] Total running time: 0h1m33s