[2023-06-13 22:54:22,096] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:54:22,098] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:54:22,098] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb6397c3-a1f8-4a82-99bd-32f9103d9437/dqc_reference
[2023-06-13 22:54:23,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:54:23,253] [INFO] Task started: Prodigal
[2023-06-13 22:54:23,253] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe831bee-dc78-4a0f-b3d9-6decc6a95761/GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:54:25,249] [INFO] Task succeeded: Prodigal
[2023-06-13 22:54:25,249] [INFO] Task started: HMMsearch
[2023-06-13 22:54:25,249] [INFO] Running command: hmmsearch --tblout GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb6397c3-a1f8-4a82-99bd-32f9103d9437/dqc_reference/reference_markers.hmm GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:54:25,479] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:54:25,480] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfe831bee-dc78-4a0f-b3d9-6decc6a95761/GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 22:54:25,497] [INFO] Query marker FASTA was written to GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 22:54:25,497] [INFO] Task started: Blastn
[2023-06-13 22:54:25,497] [INFO] Running command: blastn -query GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb6397c3-a1f8-4a82-99bd-32f9103d9437/dqc_reference/reference_markers.fasta -out GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:54:26,014] [INFO] Task succeeded: Blastn
[2023-06-13 22:54:26,017] [INFO] Selected 20 target genomes.
[2023-06-13 22:54:26,018] [INFO] Target genome list was writen to GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 22:54:26,019] [INFO] Task started: fastANI
[2023-06-13 22:54:26,019] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe831bee-dc78-4a0f-b3d9-6decc6a95761/GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:54:35,205] [INFO] Task succeeded: fastANI
[2023-06-13 22:54:35,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb6397c3-a1f8-4a82-99bd-32f9103d9437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:54:35,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb6397c3-a1f8-4a82-99bd-32f9103d9437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:54:35,210] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:54:35,210] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 22:54:35,210] [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
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	75.1136	54	469	95	below_threshold
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	75.0773	56	469	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	75.0012	51	469	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:54:35,212] [INFO] DFAST Taxonomy check result was written to GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 22:54:35,212] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:54:35,213] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:54:35,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb6397c3-a1f8-4a82-99bd-32f9103d9437/dqc_reference/checkm_data
[2023-06-13 22:54:35,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:54:35,231] [INFO] Task started: CheckM
[2023-06-13 22:54:35,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 22:54:48,508] [INFO] Task succeeded: CheckM
[2023-06-13 22:54:48,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 22:54:48,526] [INFO] ===== Completeness check finished =====
[2023-06-13 22:54:48,526] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:54:48,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 22:54:48,526] [INFO] Task started: Blastn
[2023-06-13 22:54:48,526] [INFO] Running command: blastn -query GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb6397c3-a1f8-4a82-99bd-32f9103d9437/dqc_reference/reference_markers_gtdb.fasta -out GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:54:49,218] [INFO] Task succeeded: Blastn
[2023-06-13 22:54:49,221] [INFO] Selected 12 target genomes.
[2023-06-13 22:54:49,221] [INFO] Target genome list was writen to GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:54:49,222] [INFO] Task started: fastANI
[2023-06-13 22:54:49,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe831bee-dc78-4a0f-b3d9-6decc6a95761/GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:54:52,910] [INFO] Task succeeded: fastANI
[2023-06-13 22:54:52,919] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 22:54:52,919] [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_000431335.1	s__CAG-269 sp000431335	98.7053	382	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.17	98.64	0.90	0.86	6	conclusive
GCA_900556945.1	s__CAG-269 sp900556945	82.365	168	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.30	99.23	0.81	0.81	3	-
GCA_900556695.1	s__CAG-269 sp900556695	81.0554	179	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905213875.1	s__CAG-269 sp905213875	80.9803	255	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.16	98.07	0.72	0.64	3	-
GCA_900554565.1	s__CAG-269 sp900554565	80.8369	253	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.93	97.94	0.90	0.85	3	-
GCA_900554365.1	s__CAG-269 sp900554365	80.2645	213	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900762425.1	s__CAG-269 sp900762425	80.2083	243	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215845.1	s__CAG-269 sp905215845	80.1688	134	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014846485.1	s__CAG-269 sp014846485	80.1446	219	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001916005.1	s__CAG-269 sp001916005	79.5791	216	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	96.70	96.22	0.72	0.66	3	-
GCA_000437215.1	s__CAG-269 sp000437215	79.4163	221	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.98	98.94	0.85	0.85	3	-
GCA_904419495.1	s__CAG-269 sp904419495	79.2911	213	469	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 22:54:52,924] [INFO] GTDB search result was written to GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 22:54:52,925] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:54:52,928] [INFO] DFAST_QC result json was written to GCA_938045795.1_ERR688646_bin.55_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 22:54:52,928] [INFO] DFAST_QC completed!
[2023-06-13 22:54:52,928] [INFO] Total running time: 0h0m31s