[2024-01-24 11:51:37,363] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f91dcd5-836e-43fc-8b2c-381cd596fe80/dqc_reference
[2024-01-24 11:51:38,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,638] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg12c4e92b-bdca-4875-88bb-75d43e950d76/GCF_014653315.1_ASM1465331v1_genomic.fna.gz | prodigal -d GCF_014653315.1_ASM1465331v1_genomic.fna/cds.fna -a GCF_014653315.1_ASM1465331v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:46,679] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:46,679] [INFO] Task started: HMMsearch
[2024-01-24 11:51:46,680] [INFO] Running command: hmmsearch --tblout GCF_014653315.1_ASM1465331v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f91dcd5-836e-43fc-8b2c-381cd596fe80/dqc_reference/reference_markers.hmm GCF_014653315.1_ASM1465331v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:46,986] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:46,988] [INFO] Found 6/6 markers.
[2024-01-24 11:51:47,021] [INFO] Query marker FASTA was written to GCF_014653315.1_ASM1465331v1_genomic.fna/markers.fasta
[2024-01-24 11:51:47,021] [INFO] Task started: Blastn
[2024-01-24 11:51:47,021] [INFO] Running command: blastn -query GCF_014653315.1_ASM1465331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f91dcd5-836e-43fc-8b2c-381cd596fe80/dqc_reference/reference_markers.fasta -out GCF_014653315.1_ASM1465331v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:48,344] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:48,347] [INFO] Selected 19 target genomes.
[2024-01-24 11:51:48,347] [INFO] Target genome list was writen to GCF_014653315.1_ASM1465331v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:48,354] [INFO] Task started: fastANI
[2024-01-24 11:51:48,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg12c4e92b-bdca-4875-88bb-75d43e950d76/GCF_014653315.1_ASM1465331v1_genomic.fna.gz --refList GCF_014653315.1_ASM1465331v1_genomic.fna/target_genomes.txt --output GCF_014653315.1_ASM1465331v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:02,285] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:02,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f91dcd5-836e-43fc-8b2c-381cd596fe80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:02,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f91dcd5-836e-43fc-8b2c-381cd596fe80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:02,309] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:02,309] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:02,310] [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
Flavimobilis marinus	strain=CGMCC 1.3457	GCA_014653315.1	285351	285351	type	True	100.0	963	963	95	conclusive
Flavimobilis marinus	strain=DSM 19083	GCA_900113055.1	285351	285351	type	True	99.9993	959	963	95	conclusive
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	79.9547	483	963	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.9176	484	963	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	79.8984	512	963	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.8826	488	963	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	79.8466	470	963	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	79.6978	482	963	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	79.5875	472	963	95	below_threshold
Sanguibacter suaedae	strain=YZGR15	GCA_016342785.1	2795737	2795737	type	True	79.5732	450	963	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.5648	492	963	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	79.4896	551	963	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	79.4844	447	963	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.267	519	963	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	79.2386	500	963	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.2194	495	963	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.1852	489	963	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	79.1637	453	963	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.1003	455	963	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:02,311] [INFO] DFAST Taxonomy check result was written to GCF_014653315.1_ASM1465331v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:02,312] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:02,312] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:02,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f91dcd5-836e-43fc-8b2c-381cd596fe80/dqc_reference/checkm_data
[2024-01-24 11:52:02,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:02,343] [INFO] Task started: CheckM
[2024-01-24 11:52:02,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653315.1_ASM1465331v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653315.1_ASM1465331v1_genomic.fna/checkm_input GCF_014653315.1_ASM1465331v1_genomic.fna/checkm_result
[2024-01-24 11:52:43,232] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:43,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:43,252] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:43,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:43,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653315.1_ASM1465331v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:43,253] [INFO] Task started: Blastn
[2024-01-24 11:52:43,254] [INFO] Running command: blastn -query GCF_014653315.1_ASM1465331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f91dcd5-836e-43fc-8b2c-381cd596fe80/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653315.1_ASM1465331v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:45,265] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:45,269] [INFO] Selected 20 target genomes.
[2024-01-24 11:52:45,269] [INFO] Target genome list was writen to GCF_014653315.1_ASM1465331v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:45,288] [INFO] Task started: fastANI
[2024-01-24 11:52:45,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg12c4e92b-bdca-4875-88bb-75d43e950d76/GCF_014653315.1_ASM1465331v1_genomic.fna.gz --refList GCF_014653315.1_ASM1465331v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653315.1_ASM1465331v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:59,928] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:59,945] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:59,946] [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_900113055.1	s__Flavimobilis marinus	99.9993	959	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002564025.1	s__Flavimobilis soli	80.9135	578	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396185.1	s__Flavimobilis hominis	80.8266	538	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011300875.1	s__Flavimobilis sp011300875	79.993	533	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797595.1	s__Sediminihabitans luteus	79.9614	482	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000024925.1	s__Sanguibacter keddieii	79.9128	511	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001692445.1	s__Oerskovia enterophila	79.7969	474	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	98.35	97.89	0.90	0.89	4	-
GCF_014852685.1	s__Flavimobilis rhizosphaerae	79.7703	508	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	95.20	95.20	0.83	0.83	2	-
GCF_013415325.1	s__Sanguibacter inulinus	79.6877	483	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	98.94	97.89	0.97	0.94	3	-
GCF_016342785.1	s__Sanguibacter sp016342785	79.5572	451	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538745.1	s__Cellulomonas cellasea	79.4727	553	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	79.431	503	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750215.1	s__Xylanimonas variabilis_A	79.4131	396	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033115.1	s__Cellulomonas sp008033115	79.4052	501	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	96.34	96.34	0.91	0.91	2	-
GCF_016862675.1	s__Cellulomonas chitinilytica	79.2323	485	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803435.1	s__Cellulosimicrobium terreum	79.1731	494	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752595.1	s__Sediminihabitans sp003752595	79.1658	472	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017569225.1	s__Cellulomonas sp017569225	79.1021	476	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715865.1	s__Cellulomonas sp006715865	79.0987	493	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744555.1	s__Cellulomonas sp017744555	78.8483	479	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:59,947] [INFO] GTDB search result was written to GCF_014653315.1_ASM1465331v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:59,948] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:59,955] [INFO] DFAST_QC result json was written to GCF_014653315.1_ASM1465331v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:59,955] [INFO] DFAST_QC completed!
[2024-01-24 11:52:59,955] [INFO] Total running time: 0h1m23s