[2024-01-24 11:12:28,091] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg143903a5-a415-441c-9a0f-7d38a7706750/dqc_reference
[2024-01-24 11:12:29,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,523] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,523] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3fbb4fa-54c8-417d-85ea-68ba58893437/GCF_013410455.1_ASM1341045v1_genomic.fna.gz | prodigal -d GCF_013410455.1_ASM1341045v1_genomic.fna/cds.fna -a GCF_013410455.1_ASM1341045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:41,420] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:41,420] [INFO] Task started: HMMsearch
[2024-01-24 11:12:41,420] [INFO] Running command: hmmsearch --tblout GCF_013410455.1_ASM1341045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg143903a5-a415-441c-9a0f-7d38a7706750/dqc_reference/reference_markers.hmm GCF_013410455.1_ASM1341045v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:41,732] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:41,733] [INFO] Found 6/6 markers.
[2024-01-24 11:12:41,769] [INFO] Query marker FASTA was written to GCF_013410455.1_ASM1341045v1_genomic.fna/markers.fasta
[2024-01-24 11:12:41,770] [INFO] Task started: Blastn
[2024-01-24 11:12:41,770] [INFO] Running command: blastn -query GCF_013410455.1_ASM1341045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg143903a5-a415-441c-9a0f-7d38a7706750/dqc_reference/reference_markers.fasta -out GCF_013410455.1_ASM1341045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:43,190] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:43,194] [INFO] Selected 25 target genomes.
[2024-01-24 11:12:43,194] [INFO] Target genome list was writen to GCF_013410455.1_ASM1341045v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:43,203] [INFO] Task started: fastANI
[2024-01-24 11:12:43,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3fbb4fa-54c8-417d-85ea-68ba58893437/GCF_013410455.1_ASM1341045v1_genomic.fna.gz --refList GCF_013410455.1_ASM1341045v1_genomic.fna/target_genomes.txt --output GCF_013410455.1_ASM1341045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:02,950] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:02,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg143903a5-a415-441c-9a0f-7d38a7706750/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:02,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg143903a5-a415-441c-9a0f-7d38a7706750/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:02,969] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:02,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:02,969] [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
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	79.9883	503	1238	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	79.959	553	1238	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	79.8488	505	1238	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	79.5465	497	1238	95	below_threshold
Branchiibius hedensis	strain=DSM 22951	GCA_003149195.1	672460	672460	type	True	79.3034	382	1238	95	below_threshold
Branchiibius hedensis	strain=DSM 22951	GCA_900108585.1	672460	672460	type	True	79.2909	383	1238	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	79.1322	483	1238	95	below_threshold
Flexivirga endophytica	strain=KCTC 39536	GCA_014652735.1	1849103	1849103	type	True	78.9663	460	1238	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	78.9653	412	1238	95	below_threshold
Flexivirga endophytica	strain=CGMCC 1.15085	GCA_014640635.1	1849103	1849103	type	True	78.9554	469	1238	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	78.5897	317	1238	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.553	332	1238	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	78.5363	394	1238	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.426	339	1238	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.3704	405	1238	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	78.3702	354	1238	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	78.362	380	1238	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.329	352	1238	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.3161	339	1238	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	78.2666	345	1238	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.8959	338	1238	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.1163	259	1238	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	77.0356	267	1238	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	76.9382	351	1238	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	76.8302	321	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:02,971] [INFO] DFAST Taxonomy check result was written to GCF_013410455.1_ASM1341045v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:02,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:02,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:02,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg143903a5-a415-441c-9a0f-7d38a7706750/dqc_reference/checkm_data
[2024-01-24 11:13:02,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:03,020] [INFO] Task started: CheckM
[2024-01-24 11:13:03,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410455.1_ASM1341045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410455.1_ASM1341045v1_genomic.fna/checkm_input GCF_013410455.1_ASM1341045v1_genomic.fna/checkm_result
[2024-01-24 11:14:07,414] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:07,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:07,444] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:07,445] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:07,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410455.1_ASM1341045v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:07,445] [INFO] Task started: Blastn
[2024-01-24 11:14:07,446] [INFO] Running command: blastn -query GCF_013410455.1_ASM1341045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg143903a5-a415-441c-9a0f-7d38a7706750/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410455.1_ASM1341045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:09,436] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:09,442] [INFO] Selected 16 target genomes.
[2024-01-24 11:14:09,443] [INFO] Target genome list was writen to GCF_013410455.1_ASM1341045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:09,455] [INFO] Task started: fastANI
[2024-01-24 11:14:09,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3fbb4fa-54c8-417d-85ea-68ba58893437/GCF_013410455.1_ASM1341045v1_genomic.fna.gz --refList GCF_013410455.1_ASM1341045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410455.1_ASM1341045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:22,009] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:22,029] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:22,029] [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_013410455.1	s__Allobranchiibius huperziae	100.0	1238	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	97.04	97.04	0.91	0.91	2	conclusive
GCF_017565405.1	s__Allobranchiibius sp017565405	88.6676	1021	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716095.1	s__Barrientosiimonas humi	79.9665	505	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013002715.1	s__Flexivirga aerilata	79.9632	553	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386865.1	s__Yimella indica	79.62	447	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001247745.1	s__Luteipulveratus halotolerans	79.5466	497	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	79.1649	436	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190945.1	s__Luteipulveratus mongoliensis	79.0919	484	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829035.1	s__Rudaeicoccus suwonensis	78.9625	451	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Rudaeicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	78.9555	411	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_014640635.1	s__Flexivirga endophytica	78.9364	471	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007845645.1	s__Leekyejoonella antrihumi	78.8427	442	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Leekyejoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201035.1	s__Phycicoccus sp013201035	78.5139	407	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192725.1	s__Segeticoccus rhizosphaerae	78.4042	323	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Segeticoccus	95.0	99.13	99.13	0.90	0.90	2	-
GCF_000720925.1	s__Phycicoccus jejuensis	78.3511	407	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_006716185.1	s__Ornithinicoccus hortensis	78.3421	354	1238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:22,031] [INFO] GTDB search result was written to GCF_013410455.1_ASM1341045v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:22,032] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:22,036] [INFO] DFAST_QC result json was written to GCF_013410455.1_ASM1341045v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:22,036] [INFO] DFAST_QC completed!
[2024-01-24 11:14:22,036] [INFO] Total running time: 0h1m54s