[2023-06-17 03:13:53,113] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:13:53,117] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:13:53,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d44f514-d5a8-47cf-a943-a42d7b352049/dqc_reference
[2023-06-17 03:13:54,574] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:13:54,575] [INFO] Task started: Prodigal
[2023-06-17 03:13:54,575] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5777691-d24c-40e5-8774-11bddc036e5b/GCA_003511785.1_ASM351178v1_genomic.fna.gz | prodigal -d GCA_003511785.1_ASM351178v1_genomic.fna/cds.fna -a GCA_003511785.1_ASM351178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:14:01,570] [INFO] Task succeeded: Prodigal
[2023-06-17 03:14:01,571] [INFO] Task started: HMMsearch
[2023-06-17 03:14:01,571] [INFO] Running command: hmmsearch --tblout GCA_003511785.1_ASM351178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d44f514-d5a8-47cf-a943-a42d7b352049/dqc_reference/reference_markers.hmm GCA_003511785.1_ASM351178v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:14:01,814] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:14:01,816] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb5777691-d24c-40e5-8774-11bddc036e5b/GCA_003511785.1_ASM351178v1_genomic.fna.gz]
[2023-06-17 03:14:01,859] [INFO] Query marker FASTA was written to GCA_003511785.1_ASM351178v1_genomic.fna/markers.fasta
[2023-06-17 03:14:01,860] [INFO] Task started: Blastn
[2023-06-17 03:14:01,860] [INFO] Running command: blastn -query GCA_003511785.1_ASM351178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d44f514-d5a8-47cf-a943-a42d7b352049/dqc_reference/reference_markers.fasta -out GCA_003511785.1_ASM351178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:14:02,968] [INFO] Task succeeded: Blastn
[2023-06-17 03:14:02,972] [INFO] Selected 23 target genomes.
[2023-06-17 03:14:02,973] [INFO] Target genome list was writen to GCA_003511785.1_ASM351178v1_genomic.fna/target_genomes.txt
[2023-06-17 03:14:02,982] [INFO] Task started: fastANI
[2023-06-17 03:14:02,982] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5777691-d24c-40e5-8774-11bddc036e5b/GCA_003511785.1_ASM351178v1_genomic.fna.gz --refList GCA_003511785.1_ASM351178v1_genomic.fna/target_genomes.txt --output GCA_003511785.1_ASM351178v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:14:21,880] [INFO] Task succeeded: fastANI
[2023-06-17 03:14:21,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d44f514-d5a8-47cf-a943-a42d7b352049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:14:21,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d44f514-d5a8-47cf-a943-a42d7b352049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:14:21,898] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:14:21,899] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 03:14:21,899] [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
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	81.3038	487	734	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	81.2723	487	734	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	80.6547	510	734	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	80.1142	414	734	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	80.0799	479	734	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.8083	417	734	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	79.805	426	734	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.5513	358	734	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.3062	404	734	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	79.2468	381	734	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	79.1799	339	734	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.0363	364	734	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.9493	379	734	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.9492	391	734	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	78.9475	377	734	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.88	320	734	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.8709	397	734	95	below_threshold
Pontibaca methylaminivorans	strain=DSM 21219	GCA_900156525.1	515897	515897	type	True	78.8041	283	734	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.7437	311	734	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.6433	332	734	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.5166	314	734	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.3651	339	734	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.3366	293	734	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 03:14:21,901] [INFO] DFAST Taxonomy check result was written to GCA_003511785.1_ASM351178v1_genomic.fna/tc_result.tsv
[2023-06-17 03:14:21,902] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:14:21,902] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:14:21,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d44f514-d5a8-47cf-a943-a42d7b352049/dqc_reference/checkm_data
[2023-06-17 03:14:21,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:14:21,945] [INFO] Task started: CheckM
[2023-06-17 03:14:21,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003511785.1_ASM351178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003511785.1_ASM351178v1_genomic.fna/checkm_input GCA_003511785.1_ASM351178v1_genomic.fna/checkm_result
[2023-06-17 03:14:48,452] [INFO] Task succeeded: CheckM
[2023-06-17 03:14:48,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 03:14:48,477] [INFO] ===== Completeness check finished =====
[2023-06-17 03:14:48,477] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:14:48,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003511785.1_ASM351178v1_genomic.fna/markers.fasta)
[2023-06-17 03:14:48,478] [INFO] Task started: Blastn
[2023-06-17 03:14:48,478] [INFO] Running command: blastn -query GCA_003511785.1_ASM351178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d44f514-d5a8-47cf-a943-a42d7b352049/dqc_reference/reference_markers_gtdb.fasta -out GCA_003511785.1_ASM351178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:14:50,343] [INFO] Task succeeded: Blastn
[2023-06-17 03:14:50,348] [INFO] Selected 22 target genomes.
[2023-06-17 03:14:50,348] [INFO] Target genome list was writen to GCA_003511785.1_ASM351178v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:14:50,371] [INFO] Task started: fastANI
[2023-06-17 03:14:50,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5777691-d24c-40e5-8774-11bddc036e5b/GCA_003511785.1_ASM351178v1_genomic.fna.gz --refList GCA_003511785.1_ASM351178v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003511785.1_ASM351178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:15:08,260] [INFO] Task succeeded: fastANI
[2023-06-17 03:15:08,279] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 03:15:08,279] [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
GCA_003511785.1	s__UBA7951 sp003511785	100.0	715	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900109035.1	s__Cribrihabitans marinus	81.2586	488	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	80.6498	510	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	80.3343	467	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	80.1241	423	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	80.0669	418	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	80.0585	480	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	80.0021	407	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.9863	416	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	79.8211	416	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	79.6017	390	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	79.4758	431	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	79.351	386	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	79.2848	378	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094885.1	s__Salibaculum halophilum	79.2219	336	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	79.2005	383	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	79.065	292	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116585.1	s__Albibacillus kandeliae	79.0348	437	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	79.0281	423	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_900116195.1	s__Salipiger pacificus	78.9376	380	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900101505.1	s__Mameliella alba	78.8975	394	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_015223355.1	s__Salipiger pacificus_B	78.8516	378	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 03:15:08,282] [INFO] GTDB search result was written to GCA_003511785.1_ASM351178v1_genomic.fna/result_gtdb.tsv
[2023-06-17 03:15:08,283] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:15:08,291] [INFO] DFAST_QC result json was written to GCA_003511785.1_ASM351178v1_genomic.fna/dqc_result.json
[2023-06-17 03:15:08,291] [INFO] DFAST_QC completed!
[2023-06-17 03:15:08,291] [INFO] Total running time: 0h1m15s