[2024-01-25 19:58:20,569] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:20,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:20,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d31ccbd-f9bf-45aa-9172-73eb76969e68/dqc_reference
[2024-01-25 19:58:21,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:21,737] [INFO] Task started: Prodigal
[2024-01-25 19:58:21,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg26801592-5578-437d-9ee1-07099467b6e9/GCF_014645295.1_ASM1464529v1_genomic.fna.gz | prodigal -d GCF_014645295.1_ASM1464529v1_genomic.fna/cds.fna -a GCF_014645295.1_ASM1464529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:32,778] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:32,778] [INFO] Task started: HMMsearch
[2024-01-25 19:58:32,778] [INFO] Running command: hmmsearch --tblout GCF_014645295.1_ASM1464529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d31ccbd-f9bf-45aa-9172-73eb76969e68/dqc_reference/reference_markers.hmm GCF_014645295.1_ASM1464529v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:32,988] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:32,989] [INFO] Found 6/6 markers.
[2024-01-25 19:58:33,018] [INFO] Query marker FASTA was written to GCF_014645295.1_ASM1464529v1_genomic.fna/markers.fasta
[2024-01-25 19:58:33,018] [INFO] Task started: Blastn
[2024-01-25 19:58:33,018] [INFO] Running command: blastn -query GCF_014645295.1_ASM1464529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d31ccbd-f9bf-45aa-9172-73eb76969e68/dqc_reference/reference_markers.fasta -out GCF_014645295.1_ASM1464529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:33,767] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:33,770] [INFO] Selected 16 target genomes.
[2024-01-25 19:58:33,770] [INFO] Target genome list was writen to GCF_014645295.1_ASM1464529v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:33,781] [INFO] Task started: fastANI
[2024-01-25 19:58:33,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg26801592-5578-437d-9ee1-07099467b6e9/GCF_014645295.1_ASM1464529v1_genomic.fna.gz --refList GCF_014645295.1_ASM1464529v1_genomic.fna/target_genomes.txt --output GCF_014645295.1_ASM1464529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:47,083] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:47,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d31ccbd-f9bf-45aa-9172-73eb76969e68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:47,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d31ccbd-f9bf-45aa-9172-73eb76969e68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:47,094] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:58:47,094] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:47,095] [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
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	100.0	1298	1298	95	conclusive
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	99.9963	1297	1298	95	conclusive
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	81.4857	698	1298	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	81.0947	673	1298	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	80.6062	652	1298	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	80.5882	668	1298	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	80.565	672	1298	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	80.3552	637	1298	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.867	666	1298	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.2189	482	1298	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.1283	497	1298	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.1283	497	1298	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.0659	510	1298	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.0066	456	1298	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.8831	439	1298	95	below_threshold
[Luteovulum] sphaeroides subsp. megalophilum	strain=DSM 18937	GCA_900188265.1	418630	1063	type	True	78.8295	449	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:47,096] [INFO] DFAST Taxonomy check result was written to GCF_014645295.1_ASM1464529v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:47,097] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:47,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:47,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d31ccbd-f9bf-45aa-9172-73eb76969e68/dqc_reference/checkm_data
[2024-01-25 19:58:47,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:47,138] [INFO] Task started: CheckM
[2024-01-25 19:58:47,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645295.1_ASM1464529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645295.1_ASM1464529v1_genomic.fna/checkm_input GCF_014645295.1_ASM1464529v1_genomic.fna/checkm_result
[2024-01-25 19:59:29,250] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:29,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:29,265] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:29,266] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:29,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645295.1_ASM1464529v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:29,266] [INFO] Task started: Blastn
[2024-01-25 19:59:29,266] [INFO] Running command: blastn -query GCF_014645295.1_ASM1464529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d31ccbd-f9bf-45aa-9172-73eb76969e68/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645295.1_ASM1464529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:30,439] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:30,442] [INFO] Selected 12 target genomes.
[2024-01-25 19:59:30,442] [INFO] Target genome list was writen to GCF_014645295.1_ASM1464529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:30,461] [INFO] Task started: fastANI
[2024-01-25 19:59:30,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg26801592-5578-437d-9ee1-07099467b6e9/GCF_014645295.1_ASM1464529v1_genomic.fna.gz --refList GCF_014645295.1_ASM1464529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645295.1_ASM1464529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:40,744] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:40,753] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:40,753] [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_007859075.1	s__Gemmobacter aquaticus	99.9963	1297	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_008271655.1	s__Gemmobacter caeruleus	81.518	695	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652355.1	s__Gemmobacter lanyuensis	81.1078	671	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570715.1	s__Gemmobacter lutimaris	80.6014	667	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054195.1	s__Gemmobacter caeni	80.5785	655	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCF_900110025.1	s__Gemmobacter aquatilis	80.5774	671	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	80.4624	564	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973825.1	s__Gemmobacter serpentinus	80.3366	638	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003509785.1	s__Gemmobacter sp003509785	79.85	499	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	99.39	99.26	0.82	0.79	4	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	79.5052	539	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	79.1843	486	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCF_003034965.1	s__Fuscovulum blasticum	78.7407	504	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fuscovulum	95.0	97.58	97.58	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:40,755] [INFO] GTDB search result was written to GCF_014645295.1_ASM1464529v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:40,756] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:40,761] [INFO] DFAST_QC result json was written to GCF_014645295.1_ASM1464529v1_genomic.fna/dqc_result.json
[2024-01-25 19:59:40,761] [INFO] DFAST_QC completed!
[2024-01-25 19:59:40,762] [INFO] Total running time: 0h1m20s