[2024-01-24 10:47:06,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg79d2c6a0-c0cf-4a0b-bd97-143ead4836f3/dqc_reference
[2024-01-24 10:47:12,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,831] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f60fc3a-2c05-4ce1-8a5e-321f10798e1c/GCF_016586355.1_ASM1658635v1_genomic.fna.gz | prodigal -d GCF_016586355.1_ASM1658635v1_genomic.fna/cds.fna -a GCF_016586355.1_ASM1658635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:20,255] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:20,256] [INFO] Task started: HMMsearch
[2024-01-24 10:47:20,256] [INFO] Running command: hmmsearch --tblout GCF_016586355.1_ASM1658635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79d2c6a0-c0cf-4a0b-bd97-143ead4836f3/dqc_reference/reference_markers.hmm GCF_016586355.1_ASM1658635v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:20,528] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:20,529] [INFO] Found 6/6 markers.
[2024-01-24 10:47:20,558] [INFO] Query marker FASTA was written to GCF_016586355.1_ASM1658635v1_genomic.fna/markers.fasta
[2024-01-24 10:47:20,559] [INFO] Task started: Blastn
[2024-01-24 10:47:20,559] [INFO] Running command: blastn -query GCF_016586355.1_ASM1658635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79d2c6a0-c0cf-4a0b-bd97-143ead4836f3/dqc_reference/reference_markers.fasta -out GCF_016586355.1_ASM1658635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:21,260] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:21,264] [INFO] Selected 23 target genomes.
[2024-01-24 10:47:21,264] [INFO] Target genome list was writen to GCF_016586355.1_ASM1658635v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:22,468] [INFO] Task started: fastANI
[2024-01-24 10:47:22,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f60fc3a-2c05-4ce1-8a5e-321f10798e1c/GCF_016586355.1_ASM1658635v1_genomic.fna.gz --refList GCF_016586355.1_ASM1658635v1_genomic.fna/target_genomes.txt --output GCF_016586355.1_ASM1658635v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:35,922] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:35,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79d2c6a0-c0cf-4a0b-bd97-143ead4836f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:35,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79d2c6a0-c0cf-4a0b-bd97-143ead4836f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:35,938] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:35,938] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:35,939] [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
Anaerostipes butyraticus	strain=JCM 17466	GCA_016586355.1	645466	645466	type	True	100.0	1022	1029	95	conclusive
Anaerostipes faecalis	strain=AGMB03513	GCA_018982945.1	2738446	2738446	type	True	78.9837	282	1029	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	78.7693	83	1029	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	78.7514	65	1029	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	78.6893	66	1029	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.5797	85	1029	95	below_threshold
Anaerostipes hadrus	strain=DSM 3319	GCA_000332875.2	649756	649756	type	True	78.5355	227	1029	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.5059	83	1029	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	78.0019	63	1029	95	below_threshold
Anaerostipes rhamnosivorans	strain=1y2	GCA_005280655.1	1229621	1229621	type	True	77.9851	153	1029	95	below_threshold
Anaerostipes hominis	strain=BG01	GCA_002270485.1	2025494	2025494	type	True	77.9714	132	1029	95	below_threshold
Anaerostipes caccae	strain=DSM 14662	GCA_025146005.1	105841	105841	type	True	77.9324	152	1029	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.9251	73	1029	95	below_threshold
Anaerostipes caccae	strain=JCM 13470	GCA_014467075.1	105841	105841	type	True	77.9004	149	1029	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	77.6765	68	1029	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.656	66	1029	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	77.4898	54	1029	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	77.4285	55	1029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:35,942] [INFO] DFAST Taxonomy check result was written to GCF_016586355.1_ASM1658635v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:35,943] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:35,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:35,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79d2c6a0-c0cf-4a0b-bd97-143ead4836f3/dqc_reference/checkm_data
[2024-01-24 10:47:35,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:35,979] [INFO] Task started: CheckM
[2024-01-24 10:47:35,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016586355.1_ASM1658635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016586355.1_ASM1658635v1_genomic.fna/checkm_input GCF_016586355.1_ASM1658635v1_genomic.fna/checkm_result
[2024-01-24 10:48:04,857] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:04,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:04,880] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:04,880] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:04,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016586355.1_ASM1658635v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:04,881] [INFO] Task started: Blastn
[2024-01-24 10:48:04,881] [INFO] Running command: blastn -query GCF_016586355.1_ASM1658635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79d2c6a0-c0cf-4a0b-bd97-143ead4836f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016586355.1_ASM1658635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:06,047] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:06,052] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:06,052] [INFO] Target genome list was writen to GCF_016586355.1_ASM1658635v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:06,089] [INFO] Task started: fastANI
[2024-01-24 10:48:06,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f60fc3a-2c05-4ce1-8a5e-321f10798e1c/GCF_016586355.1_ASM1658635v1_genomic.fna.gz --refList GCF_016586355.1_ASM1658635v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016586355.1_ASM1658635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:16,361] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:16,381] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:16,381] [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_016586355.1	s__Anaerostipes butyraticus	100.0	1022	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.19	99.02	0.93	0.93	4	conclusive
GCA_019119895.1	s__Anaerostipes avistercoris	85.9251	741	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161065.1	s__Anaerobutyricum faecale	82.1392	97	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	98.93	98.91	0.92	0.91	3	-
GCA_019114985.1	s__Anaerostipes excrementavium	80.3779	469	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.16	98.38	0.90	0.84	3	-
GCA_900016875.1	s__Anaerobutyricum stercoris	80.1683	66	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	98.34	98.09	0.89	0.78	6	-
GCF_016902345.1	s__Mediterraneibacter glycyrrhizinilyticus_A	80.1003	58	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940315.1	s__Anaerostipes sp001940315	79.3218	268	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.20	99.20	0.89	0.89	2	-
GCF_018918155.1	s__Anaerostipes sp018918155	79.1272	251	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001404655.1	s__Anaerostipes hadrus_A	78.7726	209	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.11	98.66	0.92	0.88	9	-
GCA_900756035.1	s__Anaerostipes sp900756035	78.6207	213	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210015.1	s__Blautia_A obeum_B	78.2661	54	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.64	98.44	0.85	0.84	7	-
GCF_005280655.1	s__Anaerostipes rhamnosivorans	77.9818	152	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.93	99.92	0.96	0.94	3	-
GCA_000508985.1	s__Anaerostipes sp000508985	77.9745	133	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	98.99	98.66	0.91	0.87	11	-
GCF_000484655.1	s__Blautia_A wexlerae	77.6765	68	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	-
GCF_003574295.1	s__Mediterraneibacter_A butyricigenes	77.656	66	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter_A	95.0	98.15	98.07	0.82	0.80	5	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,383] [INFO] GTDB search result was written to GCF_016586355.1_ASM1658635v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:16,384] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:16,388] [INFO] DFAST_QC result json was written to GCF_016586355.1_ASM1658635v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:16,388] [INFO] DFAST_QC completed!
[2024-01-24 10:48:16,388] [INFO] Total running time: 0h1m10s