[2024-01-24 11:26:38,485] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,487] [INFO] DQC Reference Directory: /var/lib/cwl/stged4b0680-83f4-42f0-a99c-480c5e8f68da/dqc_reference
[2024-01-24 11:26:39,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:39,817] [INFO] Task started: Prodigal
[2024-01-24 11:26:39,817] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3148036-cf45-4968-bc7b-0ee51e1d87f7/GCF_014174405.1_ASM1417440v1_genomic.fna.gz | prodigal -d GCF_014174405.1_ASM1417440v1_genomic.fna/cds.fna -a GCF_014174405.1_ASM1417440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:48,628] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:48,629] [INFO] Task started: HMMsearch
[2024-01-24 11:26:48,629] [INFO] Running command: hmmsearch --tblout GCF_014174405.1_ASM1417440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged4b0680-83f4-42f0-a99c-480c5e8f68da/dqc_reference/reference_markers.hmm GCF_014174405.1_ASM1417440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:48,930] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:48,932] [INFO] Found 6/6 markers.
[2024-01-24 11:26:48,966] [INFO] Query marker FASTA was written to GCF_014174405.1_ASM1417440v1_genomic.fna/markers.fasta
[2024-01-24 11:26:48,967] [INFO] Task started: Blastn
[2024-01-24 11:26:48,967] [INFO] Running command: blastn -query GCF_014174405.1_ASM1417440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged4b0680-83f4-42f0-a99c-480c5e8f68da/dqc_reference/reference_markers.fasta -out GCF_014174405.1_ASM1417440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:49,602] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:49,605] [INFO] Selected 21 target genomes.
[2024-01-24 11:26:49,605] [INFO] Target genome list was writen to GCF_014174405.1_ASM1417440v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:49,615] [INFO] Task started: fastANI
[2024-01-24 11:26:49,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3148036-cf45-4968-bc7b-0ee51e1d87f7/GCF_014174405.1_ASM1417440v1_genomic.fna.gz --refList GCF_014174405.1_ASM1417440v1_genomic.fna/target_genomes.txt --output GCF_014174405.1_ASM1417440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:03,891] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:03,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged4b0680-83f4-42f0-a99c-480c5e8f68da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:03,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged4b0680-83f4-42f0-a99c-480c5e8f68da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:03,906] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:03,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:03,906] [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
Variimorphobacter saccharofermentans	strain=MD1	GCA_014174405.1	2755051	2755051	type	True	100.0	1386	1386	95	conclusive
Herbinix luporum	strain=SD1D	GCA_900070325.1	1679721	1679721	type	True	78.325	130	1386	95	below_threshold
Lachnoclostridium phytofermentans	strain=ISDg	GCA_000018685.1	66219	66219	type	True	78.2282	87	1386	95	below_threshold
Anaerocolumna sedimenticola	strain=CBA3638	GCA_009931695.1	2696063	2696063	type	True	77.9103	117	1386	95	below_threshold
Anaerocolumna chitinilytica	strain=CTTW	GCA_014218355.1	1727145	1727145	type	True	77.8969	105	1386	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	77.8921	110	1386	95	below_threshold
Mobilitalea sibirica	strain=DSM 26468	GCA_015999265.1	1462919	1462919	type	True	77.8162	211	1386	95	below_threshold
Anaerosporobacter mobilis	strain=DSM 15930	GCA_900142955.1	264463	264463	type	True	77.1218	70	1386	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	76.881	74	1386	95	below_threshold
Anaerocolumna xylanovorans	strain=DSM 12503	GCA_900143645.1	100134	100134	type	True	76.6879	91	1386	95	below_threshold
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	76.4717	70	1386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:03,908] [INFO] DFAST Taxonomy check result was written to GCF_014174405.1_ASM1417440v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:03,909] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:03,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:03,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged4b0680-83f4-42f0-a99c-480c5e8f68da/dqc_reference/checkm_data
[2024-01-24 11:27:03,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:03,957] [INFO] Task started: CheckM
[2024-01-24 11:27:03,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014174405.1_ASM1417440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014174405.1_ASM1417440v1_genomic.fna/checkm_input GCF_014174405.1_ASM1417440v1_genomic.fna/checkm_result
[2024-01-24 11:27:35,503] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:35,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:35,526] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:35,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:35,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014174405.1_ASM1417440v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:35,527] [INFO] Task started: Blastn
[2024-01-24 11:27:35,527] [INFO] Running command: blastn -query GCF_014174405.1_ASM1417440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged4b0680-83f4-42f0-a99c-480c5e8f68da/dqc_reference/reference_markers_gtdb.fasta -out GCF_014174405.1_ASM1417440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:36,654] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:36,658] [INFO] Selected 21 target genomes.
[2024-01-24 11:27:36,659] [INFO] Target genome list was writen to GCF_014174405.1_ASM1417440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:36,694] [INFO] Task started: fastANI
[2024-01-24 11:27:36,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3148036-cf45-4968-bc7b-0ee51e1d87f7/GCF_014174405.1_ASM1417440v1_genomic.fna.gz --refList GCF_014174405.1_ASM1417440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014174405.1_ASM1417440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:51,378] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:51,402] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:51,402] [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_014174405.1	s__Mobilitalea sp014174405	100.0	1386	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900070325.1	s__Mobilitalea luporum	78.2522	129	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	99.78	99.78	0.97	0.97	2	-
GCF_000702945.1	s__Anaerocolumna sp000702945	78.0362	89	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999265.1	s__Mobilitalea sibirica	77.8124	209	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003519685.1	s__Mobilitalea sp003519685	77.8115	85	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218355.1	s__Anaerocolumna sp014218355	77.7615	104	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057615.1	s__Mobilitalea sp015057615	77.7303	148	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931695.1	s__Anaerocolumna sedimenticola	77.7284	117	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017861355.1	s__Mobilitalea sp017861355	77.6681	173	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012839295.1	s__Mobilitalea sp012839295	77.5661	161	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307215.1	s__Mobilitalea sp002307215	77.5411	158	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012523775.1	s__Mobilitalea sp012523775	77.198	91	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012523925.1	s__Mobilitalea sp012523925	77.153	125	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012839085.1	s__Mobilitalea sp012839085	77.0922	129	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519905.1	s__Mobilitalea sp012519905	76.9844	103	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012070565.1	s__Anaerosporobacter sp012070565	76.4488	71	1386	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:51,404] [INFO] GTDB search result was written to GCF_014174405.1_ASM1417440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:51,404] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:51,408] [INFO] DFAST_QC result json was written to GCF_014174405.1_ASM1417440v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:51,408] [INFO] DFAST_QC completed!
[2024-01-24 11:27:51,408] [INFO] Total running time: 0h1m13s