[2023-06-30 06:01:51,673] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:01:51,676] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:01:51,676] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a216c2e-ad27-4887-bbd1-db3272bbb8f1/dqc_reference
[2023-06-30 06:01:52,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:01:52,896] [INFO] Task started: Prodigal
[2023-06-30 06:01:52,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg93b99f7f-c5c6-4573-a8cf-c4fc152f8227/GCA_024490875.1_ASM2449087v1_genomic.fna.gz | prodigal -d GCA_024490875.1_ASM2449087v1_genomic.fna/cds.fna -a GCA_024490875.1_ASM2449087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:01:55,131] [INFO] Task succeeded: Prodigal
[2023-06-30 06:01:55,132] [INFO] Task started: HMMsearch
[2023-06-30 06:01:55,132] [INFO] Running command: hmmsearch --tblout GCA_024490875.1_ASM2449087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a216c2e-ad27-4887-bbd1-db3272bbb8f1/dqc_reference/reference_markers.hmm GCA_024490875.1_ASM2449087v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:01:55,330] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:01:55,332] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg93b99f7f-c5c6-4573-a8cf-c4fc152f8227/GCA_024490875.1_ASM2449087v1_genomic.fna.gz]
[2023-06-30 06:01:55,370] [INFO] Query marker FASTA was written to GCA_024490875.1_ASM2449087v1_genomic.fna/markers.fasta
[2023-06-30 06:01:55,371] [INFO] Task started: Blastn
[2023-06-30 06:01:55,371] [INFO] Running command: blastn -query GCA_024490875.1_ASM2449087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a216c2e-ad27-4887-bbd1-db3272bbb8f1/dqc_reference/reference_markers.fasta -out GCA_024490875.1_ASM2449087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:01:55,875] [INFO] Task succeeded: Blastn
[2023-06-30 06:01:55,880] [INFO] Selected 7 target genomes.
[2023-06-30 06:01:55,880] [INFO] Target genome list was writen to GCA_024490875.1_ASM2449087v1_genomic.fna/target_genomes.txt
[2023-06-30 06:01:55,884] [INFO] Task started: fastANI
[2023-06-30 06:01:55,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg93b99f7f-c5c6-4573-a8cf-c4fc152f8227/GCA_024490875.1_ASM2449087v1_genomic.fna.gz --refList GCA_024490875.1_ASM2449087v1_genomic.fna/target_genomes.txt --output GCA_024490875.1_ASM2449087v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:01:57,998] [INFO] Task succeeded: fastANI
[2023-06-30 06:01:57,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a216c2e-ad27-4887-bbd1-db3272bbb8f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:01:57,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a216c2e-ad27-4887-bbd1-db3272bbb8f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:01:58,010] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:01:58,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 06:01:58,010] [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
Methanocaldococcus bathoardescens	strain=JH146	GCA_000739065.1	1301915	1301915	type	True	81.1379	331	467	95	below_threshold
Methanocaldococcus jannaschii	strain=DSM 2661	GCA_000091665.1	2190	2190	type	True	79.8958	312	467	95	below_threshold
Methanocaldococcus fervens	strain=AG86	GCA_000023985.1	83171	83171	type	True	79.3703	259	467	95	below_threshold
Methanocaldococcus villosus	strain=KIN24-T80	GCA_000363885.1	667126	667126	type	True	77.1076	122	467	95	below_threshold
Methanocaldococcus villosus	strain=KIN24-T80	GCA_000371805.1	667126	667126	type	True	77.012	129	467	95	below_threshold
Methanocaldococcus infernus	strain=ME	GCA_000092305.1	67760	67760	type	True	76.9295	91	467	95	below_threshold
Methanothermococcus okinawensis	strain=IH1	GCA_000179575.2	155863	155863	type	True	75.9513	75	467	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 06:01:58,012] [INFO] DFAST Taxonomy check result was written to GCA_024490875.1_ASM2449087v1_genomic.fna/tc_result.tsv
[2023-06-30 06:01:58,013] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:01:58,013] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:01:58,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a216c2e-ad27-4887-bbd1-db3272bbb8f1/dqc_reference/checkm_data
[2023-06-30 06:01:58,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:01:58,035] [INFO] Task started: CheckM
[2023-06-30 06:01:58,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024490875.1_ASM2449087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024490875.1_ASM2449087v1_genomic.fna/checkm_input GCA_024490875.1_ASM2449087v1_genomic.fna/checkm_result
[2023-06-30 06:02:12,897] [INFO] Task succeeded: CheckM
[2023-06-30 06:02:12,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:02:12,921] [INFO] ===== Completeness check finished =====
[2023-06-30 06:02:12,921] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:02:12,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024490875.1_ASM2449087v1_genomic.fna/markers.fasta)
[2023-06-30 06:02:12,922] [INFO] Task started: Blastn
[2023-06-30 06:02:12,922] [INFO] Running command: blastn -query GCA_024490875.1_ASM2449087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a216c2e-ad27-4887-bbd1-db3272bbb8f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_024490875.1_ASM2449087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:02:13,419] [INFO] Task succeeded: Blastn
[2023-06-30 06:02:13,424] [INFO] Selected 7 target genomes.
[2023-06-30 06:02:13,425] [INFO] Target genome list was writen to GCA_024490875.1_ASM2449087v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:02:13,451] [INFO] Task started: fastANI
[2023-06-30 06:02:13,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg93b99f7f-c5c6-4573-a8cf-c4fc152f8227/GCA_024490875.1_ASM2449087v1_genomic.fna.gz --refList GCA_024490875.1_ASM2449087v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024490875.1_ASM2449087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:02:15,756] [INFO] Task succeeded: fastANI
[2023-06-30 06:02:15,768] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 06:02:15,768] [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_902827205.1	s__Methanocaldococcus sp902827205	94.7244	391	467	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	97.43	97.43	0.94	0.94	2	-
GCF_000739065.1	s__Methanocaldococcus bathoardescens	81.1581	330	467	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000091665.1	s__Methanocaldococcus jannaschii	79.8471	315	467	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000023985.1	s__Methanocaldococcus fervens	79.3128	261	467	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000371805.1	s__Methanocaldococcus_A villosus	77.0523	127	467	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000092305.1	s__Methanocaldococcus_A infernus	76.9501	92	467	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179575.2	s__Methanothermococcus_A okinawensis	75.9335	76	467	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanothermococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:02:15,771] [INFO] GTDB search result was written to GCA_024490875.1_ASM2449087v1_genomic.fna/result_gtdb.tsv
[2023-06-30 06:02:15,771] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:02:15,774] [INFO] DFAST_QC result json was written to GCA_024490875.1_ASM2449087v1_genomic.fna/dqc_result.json
[2023-06-30 06:02:15,774] [INFO] DFAST_QC completed!
[2023-06-30 06:02:15,774] [INFO] Total running time: 0h0m24s