[2023-06-08 13:33:29,545] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:33:29,547] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:33:29,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg238b1ba9-b204-4348-b115-7f0dd4242f23/dqc_reference
[2023-06-08 13:33:30,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:33:30,865] [INFO] Task started: Prodigal
[2023-06-08 13:33:30,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg790c2ec1-7a2a-4c31-8f8d-3a4f150c5b89/GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:33:34,745] [INFO] Task succeeded: Prodigal
[2023-06-08 13:33:34,746] [INFO] Task started: HMMsearch
[2023-06-08 13:33:34,746] [INFO] Running command: hmmsearch --tblout GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg238b1ba9-b204-4348-b115-7f0dd4242f23/dqc_reference/reference_markers.hmm GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:33:34,979] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:33:34,981] [INFO] Found 6/6 markers.
[2023-06-08 13:33:35,003] [INFO] Query marker FASTA was written to GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 13:33:35,004] [INFO] Task started: Blastn
[2023-06-08 13:33:35,004] [INFO] Running command: blastn -query GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg238b1ba9-b204-4348-b115-7f0dd4242f23/dqc_reference/reference_markers.fasta -out GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:33:35,585] [INFO] Task succeeded: Blastn
[2023-06-08 13:33:35,589] [INFO] Selected 18 target genomes.
[2023-06-08 13:33:35,589] [INFO] Target genome list was writen to GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 13:33:35,592] [INFO] Task started: fastANI
[2023-06-08 13:33:35,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg790c2ec1-7a2a-4c31-8f8d-3a4f150c5b89/GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:33:47,206] [INFO] Task succeeded: fastANI
[2023-06-08 13:33:47,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg238b1ba9-b204-4348-b115-7f0dd4242f23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:33:47,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg238b1ba9-b204-4348-b115-7f0dd4242f23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:33:47,209] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:33:47,209] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 13:33:47,209] [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
--------------------------------------------------------------------------------
[2023-06-08 13:33:47,211] [INFO] DFAST Taxonomy check result was written to GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 13:33:47,212] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:33:47,212] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:33:47,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg238b1ba9-b204-4348-b115-7f0dd4242f23/dqc_reference/checkm_data
[2023-06-08 13:33:47,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:33:47,233] [INFO] Task started: CheckM
[2023-06-08 13:33:47,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 13:34:06,488] [INFO] Task succeeded: CheckM
[2023-06-08 13:34:06,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:34:06,510] [INFO] ===== Completeness check finished =====
[2023-06-08 13:34:06,510] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:34:06,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 13:34:06,511] [INFO] Task started: Blastn
[2023-06-08 13:34:06,511] [INFO] Running command: blastn -query GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg238b1ba9-b204-4348-b115-7f0dd4242f23/dqc_reference/reference_markers_gtdb.fasta -out GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:34:07,375] [INFO] Task succeeded: Blastn
[2023-06-08 13:34:07,379] [INFO] Selected 20 target genomes.
[2023-06-08 13:34:07,380] [INFO] Target genome list was writen to GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:34:07,384] [INFO] Task started: fastANI
[2023-06-08 13:34:07,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg790c2ec1-7a2a-4c31-8f8d-3a4f150c5b89/GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:34:13,882] [INFO] Task succeeded: fastANI
[2023-06-08 13:34:13,896] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:34:13,897] [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_004556755.1	s__F23-B02 sp004556755	98.9648	434	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.59	98.13	0.93	0.87	10	conclusive
GCA_000431075.1	s__F23-B02 sp000431075	79.3273	189	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	97.48	96.66	0.87	0.84	6	-
GCA_900760205.1	s__F23-B02 sp900760205	79.3076	146	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.80	98.80	0.91	0.91	2	-
GCA_016292445.1	s__F23-B02 sp016292445	79.1054	155	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	97.48	96.04	0.83	0.83	3	-
GCA_004558025.1	s__F23-B02 sp004558025	78.8512	181	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	99.18	99.18	0.86	0.86	2	-
GCA_002472405.1	s__F23-B02 sp002472405	78.8281	171	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.11	97.78	0.86	0.83	6	-
GCA_001916715.1	s__F23-B02 sp001916715	78.8142	182	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.22	97.52	0.91	0.88	7	-
GCA_900545805.1	s__F23-B02 sp900545805	78.727	154	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	99.34	98.77	0.94	0.94	3	-
GCA_900556535.1	s__F23-B02 sp900556535	78.703	144	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	99.80	99.80	0.83	0.83	2	-
GCA_004553495.1	s__F23-B02 sp004553495	78.6534	148	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.58	98.56	0.81	0.81	3	-
GCA_900772725.1	s__F23-B02 sp900772725	78.4176	130	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002314685.1	s__F23-B02 sp002314685	78.297	128	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556965.1	s__CAG-103 sp004556965	77.4269	76	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.49	98.32	0.91	0.88	6	-
GCA_018711755.1	s__Limivicinus faecipullorum	77.2207	60	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900763675.1	s__UBA738 sp900763675	76.8605	57	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546615.1	s__Scatomorpha pullistercoris	76.5166	71	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	99.45	98.95	0.93	0.93	3	-
GCA_900752445.1	s__Scatomorpha sp900752445	76.2271	67	451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	99.73	99.73	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-08 13:34:13,899] [INFO] GTDB search result was written to GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 13:34:13,899] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:34:13,902] [INFO] DFAST_QC result json was written to GCA_945965185.1_ERR2020022_bin.6_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 13:34:13,902] [INFO] DFAST_QC completed!
[2023-06-08 13:34:13,903] [INFO] Total running time: 0h0m44s