[2024-01-25 17:48:35,714] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:35,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:35,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg837aec48-9d29-4c2c-8523-c699c436c415/dqc_reference
[2024-01-25 17:48:36,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:36,857] [INFO] Task started: Prodigal
[2024-01-25 17:48:36,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg46a97fb7-00f4-4a90-a6db-bd76b463e7ff/GCF_014652195.1_ASM1465219v1_genomic.fna.gz | prodigal -d GCF_014652195.1_ASM1465219v1_genomic.fna/cds.fna -a GCF_014652195.1_ASM1465219v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:50,618] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:50,619] [INFO] Task started: HMMsearch
[2024-01-25 17:48:50,619] [INFO] Running command: hmmsearch --tblout GCF_014652195.1_ASM1465219v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg837aec48-9d29-4c2c-8523-c699c436c415/dqc_reference/reference_markers.hmm GCF_014652195.1_ASM1465219v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:50,901] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:50,902] [INFO] Found 6/6 markers.
[2024-01-25 17:48:50,945] [INFO] Query marker FASTA was written to GCF_014652195.1_ASM1465219v1_genomic.fna/markers.fasta
[2024-01-25 17:48:50,946] [INFO] Task started: Blastn
[2024-01-25 17:48:50,946] [INFO] Running command: blastn -query GCF_014652195.1_ASM1465219v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg837aec48-9d29-4c2c-8523-c699c436c415/dqc_reference/reference_markers.fasta -out GCF_014652195.1_ASM1465219v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:51,811] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:51,813] [INFO] Selected 13 target genomes.
[2024-01-25 17:48:51,814] [INFO] Target genome list was writen to GCF_014652195.1_ASM1465219v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:51,822] [INFO] Task started: fastANI
[2024-01-25 17:48:51,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg46a97fb7-00f4-4a90-a6db-bd76b463e7ff/GCF_014652195.1_ASM1465219v1_genomic.fna.gz --refList GCF_014652195.1_ASM1465219v1_genomic.fna/target_genomes.txt --output GCF_014652195.1_ASM1465219v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:04,796] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:04,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg837aec48-9d29-4c2c-8523-c699c436c415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:04,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg837aec48-9d29-4c2c-8523-c699c436c415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:04,805] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:49:04,805] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:04,805] [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 caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	98.2627	1318	1680	95	conclusive
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	98.1823	1335	1680	95	conclusive
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	91.1993	1224	1680	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	83.6984	928	1680	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	81.6424	784	1680	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	81.5579	905	1680	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	81.2671	800	1680	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	80.2086	701	1680	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	80.1973	702	1680	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.992	587	1680	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.7788	619	1680	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.2363	540	1680	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	79.0487	607	1680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:04,806] [INFO] DFAST Taxonomy check result was written to GCF_014652195.1_ASM1465219v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:04,808] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:04,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:04,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg837aec48-9d29-4c2c-8523-c699c436c415/dqc_reference/checkm_data
[2024-01-25 17:49:04,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:04,862] [INFO] Task started: CheckM
[2024-01-25 17:49:04,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652195.1_ASM1465219v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652195.1_ASM1465219v1_genomic.fna/checkm_input GCF_014652195.1_ASM1465219v1_genomic.fna/checkm_result
[2024-01-25 17:49:54,825] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:54,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:54,842] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:54,842] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:54,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652195.1_ASM1465219v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:54,842] [INFO] Task started: Blastn
[2024-01-25 17:49:54,843] [INFO] Running command: blastn -query GCF_014652195.1_ASM1465219v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg837aec48-9d29-4c2c-8523-c699c436c415/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652195.1_ASM1465219v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:56,523] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:56,526] [INFO] Selected 13 target genomes.
[2024-01-25 17:49:56,526] [INFO] Target genome list was writen to GCF_014652195.1_ASM1465219v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:56,540] [INFO] Task started: fastANI
[2024-01-25 17:49:56,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg46a97fb7-00f4-4a90-a6db-bd76b463e7ff/GCF_014652195.1_ASM1465219v1_genomic.fna.gz --refList GCF_014652195.1_ASM1465219v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652195.1_ASM1465219v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:09,161] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:09,169] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:09,170] [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_003054195.1	s__Gemmobacter caeni	98.2641	1318	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	conclusive
GCF_003570715.1	s__Gemmobacter lutimaris	91.1992	1224	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271655.1	s__Gemmobacter caeruleus	83.6692	932	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	82.1457	861	1680	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	81.8218	654	1680	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	81.642	784	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	81.5798	901	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008973825.1	s__Gemmobacter serpentinus	81.2715	801	1680	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	81.1058	655	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	99.39	99.26	0.82	0.79	4	-
GCF_007859075.1	s__Gemmobacter aquaticus	80.5612	674	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	79.984	689	1680	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_002336845.1	s__UBA1943 sp002336845	79.4352	554	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765795.1	s__UBA1943 sp016765795	79.0862	601	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:09,171] [INFO] GTDB search result was written to GCF_014652195.1_ASM1465219v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:09,171] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:09,174] [INFO] DFAST_QC result json was written to GCF_014652195.1_ASM1465219v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:09,174] [INFO] DFAST_QC completed!
[2024-01-25 17:50:09,174] [INFO] Total running time: 0h1m33s