[2023-06-28 18:01:49,683] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:01:49,686] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:01:49,686] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdc55eb7-b67e-4cab-9b52-7d22476f7b0e/dqc_reference
[2023-06-28 18:01:51,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:01:51,750] [INFO] Task started: Prodigal
[2023-06-28 18:01:51,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg4722e950-ee76-4f5c-8d33-6d9f5362f5d3/GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:02:06,149] [INFO] Task succeeded: Prodigal
[2023-06-28 18:02:06,150] [INFO] Task started: HMMsearch
[2023-06-28 18:02:06,150] [INFO] Running command: hmmsearch --tblout GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdc55eb7-b67e-4cab-9b52-7d22476f7b0e/dqc_reference/reference_markers.hmm GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:02:06,398] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:02:06,400] [INFO] Found 6/6 markers.
[2023-06-28 18:02:06,429] [INFO] Query marker FASTA was written to GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 18:02:06,430] [INFO] Task started: Blastn
[2023-06-28 18:02:06,430] [INFO] Running command: blastn -query GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdc55eb7-b67e-4cab-9b52-7d22476f7b0e/dqc_reference/reference_markers.fasta -out GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:02:07,022] [INFO] Task succeeded: Blastn
[2023-06-28 18:02:07,027] [INFO] Selected 17 target genomes.
[2023-06-28 18:02:07,027] [INFO] Target genome list was writen to GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 18:02:07,030] [INFO] Task started: fastANI
[2023-06-28 18:02:07,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg4722e950-ee76-4f5c-8d33-6d9f5362f5d3/GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:02:15,200] [INFO] Task succeeded: fastANI
[2023-06-28 18:02:15,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdc55eb7-b67e-4cab-9b52-7d22476f7b0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:02:15,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdc55eb7-b67e-4cab-9b52-7d22476f7b0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:02:15,212] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:02:15,212] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:02:15,213] [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
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	78.517	99	842	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	78.4154	118	842	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	78.3569	102	842	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	78.2332	105	842	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	77.7728	147	842	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	76.9649	80	842	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	76.1079	54	842	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	76.051	56	842	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:02:15,217] [INFO] DFAST Taxonomy check result was written to GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 18:02:15,218] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:02:15,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:02:15,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdc55eb7-b67e-4cab-9b52-7d22476f7b0e/dqc_reference/checkm_data
[2023-06-28 18:02:15,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:02:15,254] [INFO] Task started: CheckM
[2023-06-28 18:02:15,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 18:02:58,509] [INFO] Task succeeded: CheckM
[2023-06-28 18:02:58,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:02:58,533] [INFO] ===== Completeness check finished =====
[2023-06-28 18:02:58,533] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:02:58,534] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 18:02:58,534] [INFO] Task started: Blastn
[2023-06-28 18:02:58,534] [INFO] Running command: blastn -query GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdc55eb7-b67e-4cab-9b52-7d22476f7b0e/dqc_reference/reference_markers_gtdb.fasta -out GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:02:59,396] [INFO] Task succeeded: Blastn
[2023-06-28 18:02:59,401] [INFO] Selected 17 target genomes.
[2023-06-28 18:02:59,402] [INFO] Target genome list was writen to GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:02:59,457] [INFO] Task started: fastANI
[2023-06-28 18:02:59,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg4722e950-ee76-4f5c-8d33-6d9f5362f5d3/GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:03:06,763] [INFO] Task succeeded: fastANI
[2023-06-28 18:03:06,789] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:03:06,789] [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_001689535.1	s__Paramuribaculum sp001689535	98.7589	707	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.63	98.52	0.86	0.84	5	conclusive
GCA_009775605.1	s__Paramuribaculum sp009775605	90.7913	583	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	99.73	99.73	0.91	0.91	2	-
GCA_900551515.1	s__Paramuribaculum sp900551515	78.2136	142	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759915.1	s__Paramuribaculum sp900759915	78.0125	134	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.33	0.87	0.87	2	-
GCA_910587185.1	s__Paramuribaculum sp910587185	77.9568	136	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	96.59	96.53	0.88	0.86	5	-
GCA_014801655.1	s__Paramuribaculum sp014801655	77.8098	144	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.11	0.75	0.73	4	-
GCA_910586565.1	s__UBA7173 sp910586565	77.6385	127	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589485.1	s__Duncaniella sp910589485	77.6366	123	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586895.1	s__Paramuribaculum sp910586895	77.6241	138	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586475.1	s__Paramuribaculum sp910586475	77.4851	90	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589095.1	s__Paramuribaculum sp910589095	77.4237	94	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544535.1	s__Duncaniella sp900544535	77.4219	104	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910586665.1	s__Duncaniella sp910586665	77.4024	121	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689445.1	s__M3 sp001689445	77.3071	114	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__M3	95.0	99.97	99.97	0.98	0.98	2	-
GCA_910578805.1	s__Paramuribaculum sp910578805	77.2297	132	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689485.1	s__UBA7173 sp001689485	77.0097	92	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.04	99.00	0.86	0.84	5	-
GCA_910578305.1	s__Paramuribaculum sp910578305	76.9632	132	842	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:03:06,792] [INFO] GTDB search result was written to GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 18:03:06,792] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:03:06,796] [INFO] DFAST_QC result json was written to GCA_948468445.1_SRR18243799_bin.28_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 18:03:06,796] [INFO] DFAST_QC completed!
[2023-06-28 18:03:06,796] [INFO] Total running time: 0h1m17s