[2023-06-19 14:29:25,633] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:29:25,635] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:29:25,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg66fad4e1-00a9-4d33-9bdd-cfe4b5ab8c72/dqc_reference
[2023-06-19 14:29:26,939] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:29:26,940] [INFO] Task started: Prodigal
[2023-06-19 14:29:26,940] [INFO] Running command: gunzip -c /var/lib/cwl/stga81a5f8e-bec2-4f9e-98e7-9f4537d894be/GCA_013693875.1_ASM1369387v1_genomic.fna.gz | prodigal -d GCA_013693875.1_ASM1369387v1_genomic.fna/cds.fna -a GCA_013693875.1_ASM1369387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:29:39,947] [INFO] Task succeeded: Prodigal
[2023-06-19 14:29:39,947] [INFO] Task started: HMMsearch
[2023-06-19 14:29:39,948] [INFO] Running command: hmmsearch --tblout GCA_013693875.1_ASM1369387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66fad4e1-00a9-4d33-9bdd-cfe4b5ab8c72/dqc_reference/reference_markers.hmm GCA_013693875.1_ASM1369387v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:29:40,228] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:29:40,231] [INFO] Found 6/6 markers.
[2023-06-19 14:29:40,274] [INFO] Query marker FASTA was written to GCA_013693875.1_ASM1369387v1_genomic.fna/markers.fasta
[2023-06-19 14:29:40,275] [INFO] Task started: Blastn
[2023-06-19 14:29:40,275] [INFO] Running command: blastn -query GCA_013693875.1_ASM1369387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66fad4e1-00a9-4d33-9bdd-cfe4b5ab8c72/dqc_reference/reference_markers.fasta -out GCA_013693875.1_ASM1369387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:29:41,202] [INFO] Task succeeded: Blastn
[2023-06-19 14:29:41,207] [INFO] Selected 27 target genomes.
[2023-06-19 14:29:41,208] [INFO] Target genome list was writen to GCA_013693875.1_ASM1369387v1_genomic.fna/target_genomes.txt
[2023-06-19 14:29:41,213] [INFO] Task started: fastANI
[2023-06-19 14:29:41,213] [INFO] Running command: fastANI --query /var/lib/cwl/stga81a5f8e-bec2-4f9e-98e7-9f4537d894be/GCA_013693875.1_ASM1369387v1_genomic.fna.gz --refList GCA_013693875.1_ASM1369387v1_genomic.fna/target_genomes.txt --output GCA_013693875.1_ASM1369387v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:30:03,774] [INFO] Task succeeded: fastANI
[2023-06-19 14:30:03,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66fad4e1-00a9-4d33-9bdd-cfe4b5ab8c72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:30:03,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66fad4e1-00a9-4d33-9bdd-cfe4b5ab8c72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:30:03,794] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:30:03,794] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:30:03,794] [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
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	80.5564	698	1420	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	80.4433	703	1420	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	80.0264	669	1420	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	80.0134	642	1420	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	80.0133	652	1420	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.9645	657	1420	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	79.762	661	1420	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.5098	632	1420	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	79.4161	559	1420	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	79.4126	626	1420	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.3945	621	1420	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.3733	534	1420	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.3599	572	1420	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	79.3506	533	1420	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	79.2939	580	1420	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	79.2886	631	1420	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	79.1526	555	1420	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	79.0771	601	1420	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	79.0731	558	1420	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	79.0555	560	1420	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	78.9721	507	1420	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	78.944	513	1420	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	78.9123	517	1420	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	78.6329	559	1420	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.5218	497	1420	95	below_threshold
Gemmobacter megaterium	strain=CGMCC 1.11024	GCA_014636395.1	1086013	1086013	type	True	78.4329	439	1420	95	below_threshold
Gemmobacter megaterium	strain=DSM 26375	GCA_900156815.1	1086013	1086013	type	True	78.416	439	1420	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:30:03,797] [INFO] DFAST Taxonomy check result was written to GCA_013693875.1_ASM1369387v1_genomic.fna/tc_result.tsv
[2023-06-19 14:30:03,797] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:30:03,797] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:30:03,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66fad4e1-00a9-4d33-9bdd-cfe4b5ab8c72/dqc_reference/checkm_data
[2023-06-19 14:30:03,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:30:03,844] [INFO] Task started: CheckM
[2023-06-19 14:30:03,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013693875.1_ASM1369387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013693875.1_ASM1369387v1_genomic.fna/checkm_input GCA_013693875.1_ASM1369387v1_genomic.fna/checkm_result
[2023-06-19 14:30:52,881] [INFO] Task succeeded: CheckM
[2023-06-19 14:30:52,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:30:52,912] [INFO] ===== Completeness check finished =====
[2023-06-19 14:30:52,912] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:30:52,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013693875.1_ASM1369387v1_genomic.fna/markers.fasta)
[2023-06-19 14:30:52,913] [INFO] Task started: Blastn
[2023-06-19 14:30:52,913] [INFO] Running command: blastn -query GCA_013693875.1_ASM1369387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66fad4e1-00a9-4d33-9bdd-cfe4b5ab8c72/dqc_reference/reference_markers_gtdb.fasta -out GCA_013693875.1_ASM1369387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:30:54,420] [INFO] Task succeeded: Blastn
[2023-06-19 14:30:54,426] [INFO] Selected 22 target genomes.
[2023-06-19 14:30:54,427] [INFO] Target genome list was writen to GCA_013693875.1_ASM1369387v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:30:54,439] [INFO] Task started: fastANI
[2023-06-19 14:30:54,439] [INFO] Running command: fastANI --query /var/lib/cwl/stga81a5f8e-bec2-4f9e-98e7-9f4537d894be/GCA_013693875.1_ASM1369387v1_genomic.fna.gz --refList GCA_013693875.1_ASM1369387v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013693875.1_ASM1369387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:31:12,554] [INFO] Task succeeded: fastANI
[2023-06-19 14:31:12,572] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:31:12,572] [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_013693875.1	s__SSD5 sp013693875	100.0	1420	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SSD5	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014859945.1	s__UBA1943 sp014859945	80.8082	618	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058035.1	s__JAAKGP01 sp018058035	80.7575	634	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271465.1	s__Tabrizicola flagellata	80.5668	699	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999335.1	s__Tabrizicola soli	80.5365	722	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763725.1	s__JACXUX01 sp014763725	80.3408	493	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACXUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704435.1	s__JAAKGP01 sp016704435	80.1597	696	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	99.06	99.06	0.93	0.93	2	-
GCF_003034985.1	s__Cereibacter changlensis	79.9898	643	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCA_016793705.1	s__Tabrizicola sp016793705	79.9778	687	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	79.9689	656	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	79.9682	642	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792905.1	s__Tabrizicola sp016792905	79.9223	626	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900975.1	s__Tabrizicola aquatica	79.8738	685	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271655.1	s__Gemmobacter caeruleus	79.8102	655	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879735.1	s__Pseudogemmobacter sp014879735	79.7291	600	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	79.6175	608	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222785.1	s__Tabrizicola sp005222785	79.481	681	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016446475.1	s__Paracoccus binzhouensis	79.3268	535	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792685.1	s__Tabrizicola sp016792685	79.2606	546	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859075.1	s__Gemmobacter aquaticus	78.9036	518	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007131945.1	s__Pararhodobacter sp007131945	78.0101	364	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCA_007134405.1	s__Pararhodobacter sp007134405	77.7591	251	1420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	98.66	98.61	0.77	0.76	3	-
--------------------------------------------------------------------------------
[2023-06-19 14:31:12,574] [INFO] GTDB search result was written to GCA_013693875.1_ASM1369387v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:31:12,575] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:31:12,581] [INFO] DFAST_QC result json was written to GCA_013693875.1_ASM1369387v1_genomic.fna/dqc_result.json
[2023-06-19 14:31:12,581] [INFO] DFAST_QC completed!
[2023-06-19 14:31:12,581] [INFO] Total running time: 0h1m47s