[2024-01-24 15:02:45,861] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:45,862] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:45,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bfb41b8-a0ac-4844-91da-9ebdacec1006/dqc_reference
[2024-01-24 15:02:47,192] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:47,193] [INFO] Task started: Prodigal
[2024-01-24 15:02:47,193] [INFO] Running command: gunzip -c /var/lib/cwl/stg02d4e312-5b43-4658-b576-d01e7978f8fa/GCF_900157375.1_PRJEB19165_genomic.fna.gz | prodigal -d GCF_900157375.1_PRJEB19165_genomic.fna/cds.fna -a GCF_900157375.1_PRJEB19165_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:21,621] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:21,622] [INFO] Task started: HMMsearch
[2024-01-24 15:03:21,622] [INFO] Running command: hmmsearch --tblout GCF_900157375.1_PRJEB19165_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bfb41b8-a0ac-4844-91da-9ebdacec1006/dqc_reference/reference_markers.hmm GCF_900157375.1_PRJEB19165_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:21,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:21,975] [INFO] Found 6/6 markers.
[2024-01-24 15:03:22,033] [INFO] Query marker FASTA was written to GCF_900157375.1_PRJEB19165_genomic.fna/markers.fasta
[2024-01-24 15:03:22,034] [INFO] Task started: Blastn
[2024-01-24 15:03:22,034] [INFO] Running command: blastn -query GCF_900157375.1_PRJEB19165_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bfb41b8-a0ac-4844-91da-9ebdacec1006/dqc_reference/reference_markers.fasta -out GCF_900157375.1_PRJEB19165_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:23,299] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:23,302] [INFO] Selected 16 target genomes.
[2024-01-24 15:03:23,303] [INFO] Target genome list was writen to GCF_900157375.1_PRJEB19165_genomic.fna/target_genomes.txt
[2024-01-24 15:03:23,309] [INFO] Task started: fastANI
[2024-01-24 15:03:23,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg02d4e312-5b43-4658-b576-d01e7978f8fa/GCF_900157375.1_PRJEB19165_genomic.fna.gz --refList GCF_900157375.1_PRJEB19165_genomic.fna/target_genomes.txt --output GCF_900157375.1_PRJEB19165_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:46,553] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:46,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bfb41b8-a0ac-4844-91da-9ebdacec1006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:46,554] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bfb41b8-a0ac-4844-91da-9ebdacec1006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:46,569] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:03:46,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:03:46,570] [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
Mycobacterium shigaense	strain=UN-152	GCA_002983495.1	722731	722731	type	True	86.9043	1411	2005	95	below_threshold
Mycobacterium shigaense	strain=JCM 32072	GCA_002356315.1	722731	722731	type	True	86.8504	1439	2005	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	85.8808	1564	2005	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	84.3516	1395	2005	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	84.2778	1419	2005	95	below_threshold
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	84.1566	1384	2005	95	below_threshold
Mycobacterium florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	84.1229	1404	2005	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	83.7027	1410	2005	95	below_threshold
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	83.5641	1344	2005	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	83.3655	1289	2005	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	83.3067	1290	2005	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	83.0906	1277	2005	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	82.999	1209	2005	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	82.9917	1232	2005	95	below_threshold
Mycobacterium paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	82.5927	1302	2005	95	below_threshold
Mycobacterium paraseoulense	strain=DSM 45000	GCA_002086475.1	590652	590652	type	True	82.5872	1254	2005	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:46,572] [INFO] DFAST Taxonomy check result was written to GCF_900157375.1_PRJEB19165_genomic.fna/tc_result.tsv
[2024-01-24 15:03:46,573] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:46,573] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:46,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bfb41b8-a0ac-4844-91da-9ebdacec1006/dqc_reference/checkm_data
[2024-01-24 15:03:46,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:46,638] [INFO] Task started: CheckM
[2024-01-24 15:03:46,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900157375.1_PRJEB19165_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900157375.1_PRJEB19165_genomic.fna/checkm_input GCF_900157375.1_PRJEB19165_genomic.fna/checkm_result
[2024-01-24 15:05:16,868] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:16,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:16,896] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:16,896] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:16,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900157375.1_PRJEB19165_genomic.fna/markers.fasta)
[2024-01-24 15:05:16,897] [INFO] Task started: Blastn
[2024-01-24 15:05:16,897] [INFO] Running command: blastn -query GCF_900157375.1_PRJEB19165_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bfb41b8-a0ac-4844-91da-9ebdacec1006/dqc_reference/reference_markers_gtdb.fasta -out GCF_900157375.1_PRJEB19165_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:18,735] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:18,742] [INFO] Selected 21 target genomes.
[2024-01-24 15:05:18,742] [INFO] Target genome list was writen to GCF_900157375.1_PRJEB19165_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:18,757] [INFO] Task started: fastANI
[2024-01-24 15:05:18,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg02d4e312-5b43-4658-b576-d01e7978f8fa/GCF_900157375.1_PRJEB19165_genomic.fna.gz --refList GCF_900157375.1_PRJEB19165_genomic.fna/target_genomes_gtdb.txt --output GCF_900157375.1_PRJEB19165_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:51,574] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:51,591] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:51,591] [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_900157375.1	s__Mycobacterium rhizamassiliense	100.0	2005	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002356315.1	s__Mycobacterium shigaense	86.8447	1440	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.82	1.00	1.00	3	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	85.885	1563	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000689255.1	s__Mycobacterium triplex	84.2717	1421	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010730355.1	s__Mycobacterium florentinum	84.1442	1399	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900176255.2	s__Mycobacterium ahvazicum	83.7184	1407	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665235.1	s__Mycobacterium sp001665235	83.5324	1325	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112775.1	s__Mycobacterium montefiorense	83.4665	1350	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	83.3235	1296	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_001665835.1	s__Mycobacterium colombiense_A	83.2772	1259	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667185.1	s__Mycobacterium sp001667185	83.2545	1234	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953985.1	s__Mycobacterium colombiense_B	83.2449	1274	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_002086635.1	s__Mycobacterium alsense	83.1859	1217	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCA_002102225.1	s__Mycobacterium interjectum_B	83.1559	1253	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	83.0652	1264	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_002102255.1	s__Mycobacterium nebraskense	83.0615	1280	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCF_001954195.1	s__Mycobacterium sp001954195	83.0139	1204	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.85	0.97	0.97	2	-
GCF_001667035.1	s__Mycobacterium sp001667035	83.0044	1178	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001666835.1	s__Mycobacterium sp001666835	82.7398	1193	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCF_010731655.1	s__Mycobacterium paraseoulense	82.5991	1298	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004298145.1	s__Mycobacterium sp004298145	82.4891	1201	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:51,593] [INFO] GTDB search result was written to GCF_900157375.1_PRJEB19165_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:51,594] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:51,598] [INFO] DFAST_QC result json was written to GCF_900157375.1_PRJEB19165_genomic.fna/dqc_result.json
[2024-01-24 15:05:51,599] [INFO] DFAST_QC completed!
[2024-01-24 15:05:51,599] [INFO] Total running time: 0h3m6s