[2024-01-25 19:43:05,524] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:05,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:05,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e54df6d-940f-4ac2-b8a4-90ffc1917574/dqc_reference
[2024-01-25 19:43:06,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:06,698] [INFO] Task started: Prodigal
[2024-01-25 19:43:06,698] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb75b11d-a227-4594-a30d-625964b80515/GCF_026625565.1_ASM2662556v1_genomic.fna.gz | prodigal -d GCF_026625565.1_ASM2662556v1_genomic.fna/cds.fna -a GCF_026625565.1_ASM2662556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:39,226] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:39,227] [INFO] Task started: HMMsearch
[2024-01-25 19:43:39,227] [INFO] Running command: hmmsearch --tblout GCF_026625565.1_ASM2662556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e54df6d-940f-4ac2-b8a4-90ffc1917574/dqc_reference/reference_markers.hmm GCF_026625565.1_ASM2662556v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:39,539] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:39,540] [INFO] Found 6/6 markers.
[2024-01-25 19:43:39,600] [INFO] Query marker FASTA was written to GCF_026625565.1_ASM2662556v1_genomic.fna/markers.fasta
[2024-01-25 19:43:39,601] [INFO] Task started: Blastn
[2024-01-25 19:43:39,601] [INFO] Running command: blastn -query GCF_026625565.1_ASM2662556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e54df6d-940f-4ac2-b8a4-90ffc1917574/dqc_reference/reference_markers.fasta -out GCF_026625565.1_ASM2662556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:40,161] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:40,166] [INFO] Selected 20 target genomes.
[2024-01-25 19:43:40,166] [INFO] Target genome list was writen to GCF_026625565.1_ASM2662556v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:40,182] [INFO] Task started: fastANI
[2024-01-25 19:43:40,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb75b11d-a227-4594-a30d-625964b80515/GCF_026625565.1_ASM2662556v1_genomic.fna.gz --refList GCF_026625565.1_ASM2662556v1_genomic.fna/target_genomes.txt --output GCF_026625565.1_ASM2662556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:03,606] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:03,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e54df6d-940f-4ac2-b8a4-90ffc1917574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:03,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e54df6d-940f-4ac2-b8a4-90ffc1917574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:03,617] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:44:03,617] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:44:03,617] [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
Dyadobacter psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	79.2715	787	2562	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	78.9216	734	2562	95	below_threshold
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	78.8264	693	2562	95	below_threshold
Dyadobacter luticola	strain=T17	GCA_005860805.1	1979387	1979387	type	True	78.4319	744	2562	95	below_threshold
Dyadobacter crusticola	strain=DSM 16708	GCA_000701505.1	292407	292407	type	True	78.3836	595	2562	95	below_threshold
Dyadobacter sediminis	strain=Z12	GCA_005860765.1	1493691	1493691	type	True	78.2961	546	2562	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	78.2454	583	2562	95	below_threshold
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	78.2415	552	2562	95	below_threshold
Dyadobacter endophyticus	strain=CGMCC 1.15288	GCA_014641595.1	1749036	1749036	type	True	78.2174	741	2562	95	below_threshold
Dyadobacter beijingensis	strain=CGMCC 1.6375	GCA_014645155.1	365489	365489	type	True	78.1863	710	2562	95	below_threshold
Dyadobacter fermentans	strain=DSM 18053	GCA_000023125.1	94254	94254	type	True	78.1794	670	2562	95	below_threshold
Dyadobacter beijingensis	strain=DSM 21582	GCA_000382205.1	365489	365489	type	True	78.1723	711	2562	95	below_threshold
Dyadobacter soli	strain=DSM 25329	GCA_900101885.1	659014	659014	type	True	78.1157	727	2562	95	below_threshold
Dyadobacter psychrotolerans	strain=AR-3-6	GCA_004349265.1	2541721	2541721	type	True	78.0287	415	2562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:03,620] [INFO] DFAST Taxonomy check result was written to GCF_026625565.1_ASM2662556v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:03,620] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:03,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:03,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e54df6d-940f-4ac2-b8a4-90ffc1917574/dqc_reference/checkm_data
[2024-01-25 19:44:03,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:03,695] [INFO] Task started: CheckM
[2024-01-25 19:44:03,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026625565.1_ASM2662556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026625565.1_ASM2662556v1_genomic.fna/checkm_input GCF_026625565.1_ASM2662556v1_genomic.fna/checkm_result
[2024-01-25 19:45:32,037] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:32,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:32,056] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:32,056] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:32,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026625565.1_ASM2662556v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:32,057] [INFO] Task started: Blastn
[2024-01-25 19:45:32,057] [INFO] Running command: blastn -query GCF_026625565.1_ASM2662556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e54df6d-940f-4ac2-b8a4-90ffc1917574/dqc_reference/reference_markers_gtdb.fasta -out GCF_026625565.1_ASM2662556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:32,852] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:32,855] [INFO] Selected 19 target genomes.
[2024-01-25 19:45:32,855] [INFO] Target genome list was writen to GCF_026625565.1_ASM2662556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:32,870] [INFO] Task started: fastANI
[2024-01-25 19:45:32,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb75b11d-a227-4594-a30d-625964b80515/GCF_026625565.1_ASM2662556v1_genomic.fna.gz --refList GCF_026625565.1_ASM2662556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026625565.1_ASM2662556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:59,624] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:59,634] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:45:59,634] [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_900167945.1	s__Dyadobacter psychrophilus	79.2654	789	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428845.1	s__Dyadobacter alkalitolerans	78.9207	734	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869225.1	s__Dyadobacter bucti	78.8361	691	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898145.1	s__Dyadobacter sp001898145	78.4511	696	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	99.32	99.32	0.98	0.98	2	-
GCF_005860805.1	s__Dyadobacter luticola	78.4305	745	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701505.1	s__Dyadobacter crusticola	78.3748	598	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907165045.1	s__Dyadobacter sp907165045	78.3623	657	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369915.1	s__Dyadobacter sp008369915	78.3433	618	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860765.1	s__Dyadobacter sediminis	78.289	547	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006149045.1	s__Dyadobacter flavalbus	78.2428	584	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424405.1	s__Dyadobacter sp001424405	78.2132	610	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109045.1	s__Dyadobacter sp900109045	78.198	717	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023125.1	s__Dyadobacter fermentans	78.1902	668	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382205.1	s__Dyadobacter beijingensis	78.1774	710	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900101885.1	s__Dyadobacter soli	78.1207	726	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349265.1	s__Dyadobacter psychrotolerans	78.0238	414	2562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:59,636] [INFO] GTDB search result was written to GCF_026625565.1_ASM2662556v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:59,636] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:59,639] [INFO] DFAST_QC result json was written to GCF_026625565.1_ASM2662556v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:59,640] [INFO] DFAST_QC completed!
[2024-01-25 19:45:59,640] [INFO] Total running time: 0h2m54s