[2023-06-30 16:08:36,959] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:08:36,961] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:08:36,962] [INFO] DQC Reference Directory: /var/lib/cwl/stgaed9569d-753a-4c97-af29-1a41615d4f51/dqc_reference
[2023-06-30 16:08:38,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:08:38,083] [INFO] Task started: Prodigal
[2023-06-30 16:08:38,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgd70ea0c6-0e29-4a3d-9952-90c5ee09a18b/GCA_019421365.1_ASM1942136v1_genomic.fna.gz | prodigal -d GCA_019421365.1_ASM1942136v1_genomic.fna/cds.fna -a GCA_019421365.1_ASM1942136v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:08:45,170] [INFO] Task succeeded: Prodigal
[2023-06-30 16:08:45,170] [INFO] Task started: HMMsearch
[2023-06-30 16:08:45,170] [INFO] Running command: hmmsearch --tblout GCA_019421365.1_ASM1942136v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaed9569d-753a-4c97-af29-1a41615d4f51/dqc_reference/reference_markers.hmm GCA_019421365.1_ASM1942136v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:08:45,415] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:08:45,416] [INFO] Found 6/6 markers.
[2023-06-30 16:08:45,449] [INFO] Query marker FASTA was written to GCA_019421365.1_ASM1942136v1_genomic.fna/markers.fasta
[2023-06-30 16:08:45,450] [INFO] Task started: Blastn
[2023-06-30 16:08:45,450] [INFO] Running command: blastn -query GCA_019421365.1_ASM1942136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaed9569d-753a-4c97-af29-1a41615d4f51/dqc_reference/reference_markers.fasta -out GCA_019421365.1_ASM1942136v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:08:45,994] [INFO] Task succeeded: Blastn
[2023-06-30 16:08:45,997] [INFO] Selected 23 target genomes.
[2023-06-30 16:08:45,997] [INFO] Target genome list was writen to GCA_019421365.1_ASM1942136v1_genomic.fna/target_genomes.txt
[2023-06-30 16:08:45,999] [INFO] Task started: fastANI
[2023-06-30 16:08:45,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgd70ea0c6-0e29-4a3d-9952-90c5ee09a18b/GCA_019421365.1_ASM1942136v1_genomic.fna.gz --refList GCA_019421365.1_ASM1942136v1_genomic.fna/target_genomes.txt --output GCA_019421365.1_ASM1942136v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:08:59,188] [INFO] Task succeeded: fastANI
[2023-06-30 16:08:59,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaed9569d-753a-4c97-af29-1a41615d4f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:08:59,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaed9569d-753a-4c97-af29-1a41615d4f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:08:59,196] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:08:59,196] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:08:59,196] [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
Anaerosporobacter mobilis	strain=DSM 15930	GCA_900142955.1	264463	264463	type	True	86.884	1131	1436	95	below_threshold
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	79.6356	476	1436	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	77.0611	121	1436	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	76.8354	102	1436	95	below_threshold
[Clostridium] polysaccharolyticum	strain=DSM 1801	GCA_900111595.1	29364	29364	type	True	76.7928	72	1436	95	below_threshold
[Clostridium] populeti	strain=743A	GCA_900112775.1	37658	37658	type	True	76.5674	90	1436	95	below_threshold
Lachnoclostridium phytofermentans	strain=ISDg	GCA_000018685.1	66219	66219	type	True	76.4825	120	1436	95	below_threshold
Variimorphobacter saccharofermentans	strain=MD1	GCA_014174405.1	2755051	2755051	type	True	76.3398	55	1436	95	below_threshold
[Clostridium] fimetarium	strain=DSM 9179	GCA_900111235.1	99656	99656	type	True	75.9172	69	1436	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:08:59,198] [INFO] DFAST Taxonomy check result was written to GCA_019421365.1_ASM1942136v1_genomic.fna/tc_result.tsv
[2023-06-30 16:08:59,198] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:08:59,198] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:08:59,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaed9569d-753a-4c97-af29-1a41615d4f51/dqc_reference/checkm_data
[2023-06-30 16:08:59,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:08:59,262] [INFO] Task started: CheckM
[2023-06-30 16:08:59,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019421365.1_ASM1942136v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019421365.1_ASM1942136v1_genomic.fna/checkm_input GCA_019421365.1_ASM1942136v1_genomic.fna/checkm_result
[2023-06-30 16:09:25,111] [INFO] Task succeeded: CheckM
[2023-06-30 16:09:25,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:09:25,131] [INFO] ===== Completeness check finished =====
[2023-06-30 16:09:25,132] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:09:25,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019421365.1_ASM1942136v1_genomic.fna/markers.fasta)
[2023-06-30 16:09:25,133] [INFO] Task started: Blastn
[2023-06-30 16:09:25,133] [INFO] Running command: blastn -query GCA_019421365.1_ASM1942136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaed9569d-753a-4c97-af29-1a41615d4f51/dqc_reference/reference_markers_gtdb.fasta -out GCA_019421365.1_ASM1942136v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:09:25,891] [INFO] Task succeeded: Blastn
[2023-06-30 16:09:25,894] [INFO] Selected 20 target genomes.
[2023-06-30 16:09:25,894] [INFO] Target genome list was writen to GCA_019421365.1_ASM1942136v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:09:25,902] [INFO] Task started: fastANI
[2023-06-30 16:09:25,902] [INFO] Running command: fastANI --query /var/lib/cwl/stgd70ea0c6-0e29-4a3d-9952-90c5ee09a18b/GCA_019421365.1_ASM1942136v1_genomic.fna.gz --refList GCA_019421365.1_ASM1942136v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019421365.1_ASM1942136v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:09:40,430] [INFO] Task succeeded: fastANI
[2023-06-30 16:09:40,439] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 16:09:40,439] [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_018372435.1	s__Anaerosporobacter sp018372435	87.0799	1110	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	96.90	96.04	0.88	0.87	3	-
GCF_900142955.1	s__Anaerosporobacter mobilis	86.8751	1132	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012070565.1	s__Anaerosporobacter sp012070565	79.6518	474	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016591975.1	s__TB5 sp016591975	77.5247	173	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TB5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078195.1	s__Lachnoclostridium sp900078195	77.5193	150	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905214875.1	s__KM106-2 sp905214875	77.0881	119	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KM106-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752155.1	s__Mobilisporobacter senegalensis	77.0611	121	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003526525.1	s__Lachnoclostridium sp003526525	76.9849	77	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009731425.1	s__KM106-2 sp009731425	76.8687	146	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KM106-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115365.1	s__Anaerocolumna aminovalerica	76.8354	102	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.17	99.14	0.90	0.89	3	-
GCF_000018685.1	s__Lachnoclostridium phytofermentans	76.5004	119	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702945.1	s__Anaerocolumna sp000702945	76.1584	55	1436	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:09:40,441] [INFO] GTDB search result was written to GCA_019421365.1_ASM1942136v1_genomic.fna/result_gtdb.tsv
[2023-06-30 16:09:40,446] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:09:40,450] [INFO] DFAST_QC result json was written to GCA_019421365.1_ASM1942136v1_genomic.fna/dqc_result.json
[2023-06-30 16:09:40,450] [INFO] DFAST_QC completed!
[2023-06-30 16:09:40,450] [INFO] Total running time: 0h1m3s