[2024-01-24 10:47:06,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,560] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,560] [INFO] DQC Reference Directory: /var/lib/cwl/stge4e567f7-597c-4eca-89a1-d5d031bb9d8a/dqc_reference
[2024-01-24 10:47:11,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,933] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,934] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb38fe73-90bd-4528-9b72-6ae730253214/GCF_018982945.1_ASM1898294v1_genomic.fna.gz | prodigal -d GCF_018982945.1_ASM1898294v1_genomic.fna/cds.fna -a GCF_018982945.1_ASM1898294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:17,561] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:17,562] [INFO] Task started: HMMsearch
[2024-01-24 10:47:17,562] [INFO] Running command: hmmsearch --tblout GCF_018982945.1_ASM1898294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4e567f7-597c-4eca-89a1-d5d031bb9d8a/dqc_reference/reference_markers.hmm GCF_018982945.1_ASM1898294v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:17,816] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:17,817] [INFO] Found 6/6 markers.
[2024-01-24 10:47:17,850] [INFO] Query marker FASTA was written to GCF_018982945.1_ASM1898294v1_genomic.fna/markers.fasta
[2024-01-24 10:47:17,851] [INFO] Task started: Blastn
[2024-01-24 10:47:17,851] [INFO] Running command: blastn -query GCF_018982945.1_ASM1898294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4e567f7-597c-4eca-89a1-d5d031bb9d8a/dqc_reference/reference_markers.fasta -out GCF_018982945.1_ASM1898294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,685] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,688] [INFO] Selected 23 target genomes.
[2024-01-24 10:47:19,689] [INFO] Target genome list was writen to GCF_018982945.1_ASM1898294v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:20,984] [INFO] Task started: fastANI
[2024-01-24 10:47:20,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb38fe73-90bd-4528-9b72-6ae730253214/GCF_018982945.1_ASM1898294v1_genomic.fna.gz --refList GCF_018982945.1_ASM1898294v1_genomic.fna/target_genomes.txt --output GCF_018982945.1_ASM1898294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:34,005] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:34,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4e567f7-597c-4eca-89a1-d5d031bb9d8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:34,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4e567f7-597c-4eca-89a1-d5d031bb9d8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:34,022] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:34,022] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:34,023] [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 faecalis	strain=AGMB03513	GCA_018982945.1	2738446	2738446	type	True	100.0	830	830	95	conclusive
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	79.6016	64	830	95	below_threshold
Anaerostipes hadrus	strain=DSM 3319	GCA_000332875.2	649756	649756	type	True	79.3259	294	830	95	below_threshold
Anaerostipes butyraticus	strain=JCM 17466	GCA_016586355.1	645466	645466	type	True	78.9725	275	830	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	78.6088	56	830	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	78.0426	81	830	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	77.9992	59	830	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	77.976	62	830	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	77.963	61	830	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	77.8218	62	830	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.7259	63	830	95	below_threshold
Anaerostipes rhamnosivorans	strain=1y2	GCA_005280655.1	1229621	1229621	type	True	77.7252	110	830	95	below_threshold
Anaerostipes hominis	strain=BG01	GCA_002270485.1	2025494	2025494	type	True	77.299	111	830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:34,025] [INFO] DFAST Taxonomy check result was written to GCF_018982945.1_ASM1898294v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:34,027] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:34,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:34,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4e567f7-597c-4eca-89a1-d5d031bb9d8a/dqc_reference/checkm_data
[2024-01-24 10:47:34,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:34,060] [INFO] Task started: CheckM
[2024-01-24 10:47:34,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018982945.1_ASM1898294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018982945.1_ASM1898294v1_genomic.fna/checkm_input GCF_018982945.1_ASM1898294v1_genomic.fna/checkm_result
[2024-01-24 10:47:57,967] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:57,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:57,996] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:57,996] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:57,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018982945.1_ASM1898294v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:57,997] [INFO] Task started: Blastn
[2024-01-24 10:47:57,998] [INFO] Running command: blastn -query GCF_018982945.1_ASM1898294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4e567f7-597c-4eca-89a1-d5d031bb9d8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_018982945.1_ASM1898294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:59,074] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:59,078] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:59,078] [INFO] Target genome list was writen to GCF_018982945.1_ASM1898294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:59,203] [INFO] Task started: fastANI
[2024-01-24 10:47:59,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb38fe73-90bd-4528-9b72-6ae730253214/GCF_018982945.1_ASM1898294v1_genomic.fna.gz --refList GCF_018982945.1_ASM1898294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018982945.1_ASM1898294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:07,168] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:07,178] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:07,179] [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_001940315.1	s__Anaerostipes sp001940315	99.1514	726	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.20	99.20	0.89	0.89	2	conclusive
GCA_902362875.1	s__Anaerostipes sp900066705	80.1158	286	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.16	98.31	0.96	0.92	3	-
GCF_018918155.1	s__Anaerostipes sp018918155	79.5095	321	830	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_000332875.2	s__Anaerostipes hadrus	79.3259	294	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	98.35	97.09	0.85	0.65	78	-
GCF_001404655.1	s__Anaerostipes hadrus_A	79.2473	289	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.11	98.66	0.92	0.88	9	-
GCF_016586355.1	s__Anaerostipes butyraticus	78.9725	275	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.19	99.02	0.93	0.93	4	-
GCA_019114985.1	s__Anaerostipes excrementavium	78.9212	231	830	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_900756035.1	s__Anaerostipes sp900756035	78.8259	242	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119895.1	s__Anaerostipes avistercoris	78.7975	261	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215045.1	s__Anaerostipes sp905215045	77.9652	177	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883985.1	s__Ruminococcus_B intestinipullorum	77.9375	55	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:07,180] [INFO] GTDB search result was written to GCF_018982945.1_ASM1898294v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:07,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:07,185] [INFO] DFAST_QC result json was written to GCF_018982945.1_ASM1898294v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:07,186] [INFO] DFAST_QC completed!
[2024-01-24 10:48:07,186] [INFO] Total running time: 0h1m1s