[2024-01-24 13:40:34,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg175bc000-63f7-4cf7-9f04-190717a3f631/dqc_reference
[2024-01-24 13:40:36,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,023] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,023] [INFO] Running command: gunzip -c /var/lib/cwl/stgc65512f3-96e6-4355-a05c-777257ccab17/GCF_006439335.1_ASM643933v1_genomic.fna.gz | prodigal -d GCF_006439335.1_ASM643933v1_genomic.fna/cds.fna -a GCF_006439335.1_ASM643933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:44,183] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:44,183] [INFO] Task started: HMMsearch
[2024-01-24 13:40:44,183] [INFO] Running command: hmmsearch --tblout GCF_006439335.1_ASM643933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg175bc000-63f7-4cf7-9f04-190717a3f631/dqc_reference/reference_markers.hmm GCF_006439335.1_ASM643933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:44,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:44,502] [INFO] Found 6/6 markers.
[2024-01-24 13:40:44,539] [INFO] Query marker FASTA was written to GCF_006439335.1_ASM643933v1_genomic.fna/markers.fasta
[2024-01-24 13:40:44,539] [INFO] Task started: Blastn
[2024-01-24 13:40:44,539] [INFO] Running command: blastn -query GCF_006439335.1_ASM643933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg175bc000-63f7-4cf7-9f04-190717a3f631/dqc_reference/reference_markers.fasta -out GCF_006439335.1_ASM643933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:45,296] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:45,307] [INFO] Selected 18 target genomes.
[2024-01-24 13:40:45,307] [INFO] Target genome list was writen to GCF_006439335.1_ASM643933v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:45,340] [INFO] Task started: fastANI
[2024-01-24 13:40:45,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgc65512f3-96e6-4355-a05c-777257ccab17/GCF_006439335.1_ASM643933v1_genomic.fna.gz --refList GCF_006439335.1_ASM643933v1_genomic.fna/target_genomes.txt --output GCF_006439335.1_ASM643933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:59,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:59,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg175bc000-63f7-4cf7-9f04-190717a3f631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:59,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg175bc000-63f7-4cf7-9f04-190717a3f631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:59,295] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:59,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:59,296] [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
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	100.0	1363	1363	95	conclusive
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	79.4789	517	1363	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.5242	293	1363	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.3609	299	1363	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.3458	212	1363	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.3239	347	1363	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.1374	317	1363	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.1271	316	1363	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.9086	203	1363	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	77.7759	135	1363	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	76.4031	77	1363	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.2805	80	1363	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:59,297] [INFO] DFAST Taxonomy check result was written to GCF_006439335.1_ASM643933v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:59,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:59,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:59,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg175bc000-63f7-4cf7-9f04-190717a3f631/dqc_reference/checkm_data
[2024-01-24 13:40:59,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:59,345] [INFO] Task started: CheckM
[2024-01-24 13:40:59,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006439335.1_ASM643933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006439335.1_ASM643933v1_genomic.fna/checkm_input GCF_006439335.1_ASM643933v1_genomic.fna/checkm_result
[2024-01-24 13:41:30,131] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:30,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:30,159] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:30,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:30,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006439335.1_ASM643933v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:30,160] [INFO] Task started: Blastn
[2024-01-24 13:41:30,160] [INFO] Running command: blastn -query GCF_006439335.1_ASM643933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg175bc000-63f7-4cf7-9f04-190717a3f631/dqc_reference/reference_markers_gtdb.fasta -out GCF_006439335.1_ASM643933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:31,389] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:31,394] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:31,394] [INFO] Target genome list was writen to GCF_006439335.1_ASM643933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:31,436] [INFO] Task started: fastANI
[2024-01-24 13:41:31,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgc65512f3-96e6-4355-a05c-777257ccab17/GCF_006439335.1_ASM643933v1_genomic.fna.gz --refList GCF_006439335.1_ASM643933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006439335.1_ASM643933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:45,831] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:45,898] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:45,898] [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_006439335.1	s__Litorilituus lipolyticus	100.0	1363	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003545765.1	s__Litorilituus sp003545765	81.9732	843	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295665.1	s__Litorilituus sediminis	79.4806	516	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860755.1	s__Colwellia sp018860755	78.7202	322	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764225.1	s__Colwellia psychrerythraea_D	78.4893	348	1363	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	78.3898	372	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	78.3735	296	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885605.1	s__Colwellia ponticola	78.3609	299	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954275.1	s__Colwellia demingiae	78.3239	347	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	78.3178	299	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333305.1	s__Colwellia aromaticivorans	78.3056	293	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860915.1	s__Colwellia sp018860915	78.2569	285	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	78.2485	357	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	78.2463	358	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_900111755.1	s__Thalassotalea_D agarivorans	77.8045	134	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744155.1	s__Thalassotalea sp017744155	77.7858	143	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913705.1	s__Thalassotalea_C sp001913705	77.755	163	1363	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:45,901] [INFO] GTDB search result was written to GCF_006439335.1_ASM643933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:45,902] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:45,910] [INFO] DFAST_QC result json was written to GCF_006439335.1_ASM643933v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:45,910] [INFO] DFAST_QC completed!
[2024-01-24 13:41:45,910] [INFO] Total running time: 0h1m11s