[2023-06-28 17:05:48,255] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:05:48,259] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:05:48,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg239199fa-6834-4416-85a3-0367bd3ed889/dqc_reference
[2023-06-28 17:05:50,091] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:05:50,093] [INFO] Task started: Prodigal
[2023-06-28 17:05:50,093] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4d3f450-3d61-481d-a521-89d15c1b8a9a/GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:05:53,871] [INFO] Task succeeded: Prodigal
[2023-06-28 17:05:53,872] [INFO] Task started: HMMsearch
[2023-06-28 17:05:53,872] [INFO] Running command: hmmsearch --tblout GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg239199fa-6834-4416-85a3-0367bd3ed889/dqc_reference/reference_markers.hmm GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:05:54,053] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:05:54,054] [INFO] Found 6/6 markers.
[2023-06-28 17:05:54,075] [INFO] Query marker FASTA was written to GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 17:05:54,075] [INFO] Task started: Blastn
[2023-06-28 17:05:54,075] [INFO] Running command: blastn -query GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg239199fa-6834-4416-85a3-0367bd3ed889/dqc_reference/reference_markers.fasta -out GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:05:54,674] [INFO] Task succeeded: Blastn
[2023-06-28 17:05:54,678] [INFO] Selected 29 target genomes.
[2023-06-28 17:05:54,678] [INFO] Target genome list was writen to GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 17:05:54,683] [INFO] Task started: fastANI
[2023-06-28 17:05:54,683] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4d3f450-3d61-481d-a521-89d15c1b8a9a/GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:06:08,953] [INFO] Task succeeded: fastANI
[2023-06-28 17:06:08,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg239199fa-6834-4416-85a3-0367bd3ed889/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:06:08,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg239199fa-6834-4416-85a3-0367bd3ed889/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:06:08,962] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:06:08,962] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:06:08,962] [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
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.8953	62	490	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.8832	80	490	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	77.8133	109	490	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.6469	71	490	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.6429	62	490	95	below_threshold
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	77.3431	50	490	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.049	51	490	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:06:08,964] [INFO] DFAST Taxonomy check result was written to GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 17:06:08,965] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:06:08,965] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:06:08,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg239199fa-6834-4416-85a3-0367bd3ed889/dqc_reference/checkm_data
[2023-06-28 17:06:08,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:06:08,989] [INFO] Task started: CheckM
[2023-06-28 17:06:08,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 17:06:27,206] [INFO] Task succeeded: CheckM
[2023-06-28 17:06:27,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:06:27,226] [INFO] ===== Completeness check finished =====
[2023-06-28 17:06:27,227] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:06:27,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 17:06:27,227] [INFO] Task started: Blastn
[2023-06-28 17:06:27,227] [INFO] Running command: blastn -query GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg239199fa-6834-4416-85a3-0367bd3ed889/dqc_reference/reference_markers_gtdb.fasta -out GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:06:28,180] [INFO] Task succeeded: Blastn
[2023-06-28 17:06:28,184] [INFO] Selected 16 target genomes.
[2023-06-28 17:06:28,184] [INFO] Target genome list was writen to GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:06:28,189] [INFO] Task started: fastANI
[2023-06-28 17:06:28,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4d3f450-3d61-481d-a521-89d15c1b8a9a/GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:06:35,910] [INFO] Task succeeded: fastANI
[2023-06-28 17:06:35,917] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 17:06:35,918] [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_000020605.1	s__Agathobacter rectalis	97.7792	462	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.37	96.06	0.82	0.65	151	inconclusive
GCA_900317585.1	s__Agathobacter sp900317585	95.3007	408	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.18	95.52	0.87	0.83	5	inconclusive
GCA_900546625.1	s__Agathobacter sp900546625	94.9084	435	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	96.96	96.96	0.86	0.86	2	-
GCA_905209075.1	s__Agathobacter sp905209075	80.4331	218	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.22	97.67	0.80	0.73	5	-
GCA_900548765.1	s__Agathobacter sp900548765	78.6275	130	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	97.03	0.78	0.78	2	-
GCA_900549895.1	s__Agathobacter sp900549895	78.4648	74	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552085.1	s__Agathobacter sp900552085	77.8892	80	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
--------------------------------------------------------------------------------
[2023-06-28 17:06:35,920] [INFO] GTDB search result was written to GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 17:06:35,920] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:06:35,923] [INFO] DFAST_QC result json was written to GCA_948441605.1_SRR17622769_bin.36_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 17:06:35,923] [INFO] DFAST_QC completed!
[2023-06-28 17:06:35,924] [INFO] Total running time: 0h0m48s