[2024-01-24 15:18:51,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,882] [INFO] DQC Reference Directory: /var/lib/cwl/stgb017dcb9-f011-4a34-848e-d3be9a7360ec/dqc_reference
[2024-01-24 15:18:54,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:54,595] [INFO] Task started: Prodigal
[2024-01-24 15:18:54,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc15189a-81a8-4af5-b720-d3c0a43c2bbe/GCF_014230355.1_ASM1423035v1_genomic.fna.gz | prodigal -d GCF_014230355.1_ASM1423035v1_genomic.fna/cds.fna -a GCF_014230355.1_ASM1423035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:05,569] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:05,570] [INFO] Task started: HMMsearch
[2024-01-24 15:19:05,570] [INFO] Running command: hmmsearch --tblout GCF_014230355.1_ASM1423035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb017dcb9-f011-4a34-848e-d3be9a7360ec/dqc_reference/reference_markers.hmm GCF_014230355.1_ASM1423035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:05,885] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:05,886] [INFO] Found 6/6 markers.
[2024-01-24 15:19:05,926] [INFO] Query marker FASTA was written to GCF_014230355.1_ASM1423035v1_genomic.fna/markers.fasta
[2024-01-24 15:19:05,926] [INFO] Task started: Blastn
[2024-01-24 15:19:05,926] [INFO] Running command: blastn -query GCF_014230355.1_ASM1423035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb017dcb9-f011-4a34-848e-d3be9a7360ec/dqc_reference/reference_markers.fasta -out GCF_014230355.1_ASM1423035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:06,979] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:06,983] [INFO] Selected 16 target genomes.
[2024-01-24 15:19:06,984] [INFO] Target genome list was writen to GCF_014230355.1_ASM1423035v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:07,005] [INFO] Task started: fastANI
[2024-01-24 15:19:07,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc15189a-81a8-4af5-b720-d3c0a43c2bbe/GCF_014230355.1_ASM1423035v1_genomic.fna.gz --refList GCF_014230355.1_ASM1423035v1_genomic.fna/target_genomes.txt --output GCF_014230355.1_ASM1423035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:21,111] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:21,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb017dcb9-f011-4a34-848e-d3be9a7360ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:21,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb017dcb9-f011-4a34-848e-d3be9a7360ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:21,132] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:21,132] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:21,132] [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
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	100.0	1232	1235	95	conclusive
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	85.4344	846	1235	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	81.6194	602	1235	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	80.8056	546	1235	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	80.2791	526	1235	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	80.0799	489	1235	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	80.0351	486	1235	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	80.0255	504	1235	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	79.5912	451	1235	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	79.4702	456	1235	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	79.3508	434	1235	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	79.1464	450	1235	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	79.0652	417	1235	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.9994	449	1235	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.9254	416	1235	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.3426	376	1235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:21,134] [INFO] DFAST Taxonomy check result was written to GCF_014230355.1_ASM1423035v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:21,134] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:21,135] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:21,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb017dcb9-f011-4a34-848e-d3be9a7360ec/dqc_reference/checkm_data
[2024-01-24 15:19:21,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:21,173] [INFO] Task started: CheckM
[2024-01-24 15:19:21,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014230355.1_ASM1423035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014230355.1_ASM1423035v1_genomic.fna/checkm_input GCF_014230355.1_ASM1423035v1_genomic.fna/checkm_result
[2024-01-24 15:19:56,944] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:56,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:56,962] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:56,963] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:56,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014230355.1_ASM1423035v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:56,964] [INFO] Task started: Blastn
[2024-01-24 15:19:56,964] [INFO] Running command: blastn -query GCF_014230355.1_ASM1423035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb017dcb9-f011-4a34-848e-d3be9a7360ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_014230355.1_ASM1423035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:58,988] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:58,996] [INFO] Selected 16 target genomes.
[2024-01-24 15:19:58,997] [INFO] Target genome list was writen to GCF_014230355.1_ASM1423035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:59,008] [INFO] Task started: fastANI
[2024-01-24 15:19:59,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc15189a-81a8-4af5-b720-d3c0a43c2bbe/GCF_014230355.1_ASM1423035v1_genomic.fna.gz --refList GCF_014230355.1_ASM1423035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014230355.1_ASM1423035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:11,643] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:11,663] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:11,663] [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_014230355.1	s__Novosphingobium piscinae	100.0	1232	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014230305.1	s__Novosphingobium aerophilum	85.4197	847	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.68	98.68	0.90	0.90	2	-
GCF_014230315.1	s__Novosphingobium flavum	81.6248	601	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791705.1	s__Novosphingobium sp013791705	80.5784	430	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.87	99.87	0.91	0.91	2	-
GCF_019075875.1	s__Novosphingobium sp019075875	80.376	540	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719755.1	s__Novosphingobium sp016719755	80.3055	497	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.59	99.59	0.90	0.90	2	-
GCA_004211435.1	s__Novosphingobium sp004211435	80.1178	506	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302615.1	s__Novosphingobium sp017302615	80.0572	482	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927405.1	s__Novosphingobium olei	80.0357	503	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015661825.1	s__Novosphingobium capsulatum_A	79.7838	422	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	79.7715	501	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	79.6535	480	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141325.1	s__Novosphingobium sp013141325	79.6457	360	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454125.1	s__Novosphingobium sp002454125	79.5367	391	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822005.1	s__Novosphingobium sp013822005	79.2181	358	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	78.3706	379	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:11,665] [INFO] GTDB search result was written to GCF_014230355.1_ASM1423035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:11,666] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:11,670] [INFO] DFAST_QC result json was written to GCF_014230355.1_ASM1423035v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:11,670] [INFO] DFAST_QC completed!
[2024-01-24 15:20:11,670] [INFO] Total running time: 0h1m20s